III. Background

The continuing crisis in Somalia is multifaceted, with roots that can be traced back to the 21-year rule of President Mohamed Siad Barre (1969–1991).1 Barre’s military coup in 1969 ended Somalia’s first post-independence experiment with democratic civilian government (1960-69), a period which in later years became marked by corruption, inefficient governance, and increasingly fragmentary politics centered around clan-based political parties and patronage.2

When Siad Barre took power in 1969, he sought and obtained support from the Soviet Union and embraced “scientific socialism” for Somalia. Among his first steps were to abolish Somalia’s clan and patronage system as counter-revolutionary: a national campaign (olole) against “tribalism, corruption, nepotism, and misrule” was launched and even informal references to clan alliances were outlawed.3 A new intelligence agency, the National Security Service (NSS), was established in 1970 to monitor “security” offenses that included nepotism and tribalism.

Barre’s early rule did have some positive aspects, such as his establishment of the first written script for the Somali language, a nationwide literacy campaign (1973-75), and the empowerment of women through fairer marriage, divorce, and inheritance laws. However, his government soon degenerated into increasing dictatorship, repression, and a personality cult focused around the “Holy Trinity” of Marx, Lenin, and “the Beneficent Leader” Barre, who established an increasingly repressive and authoritarian security state, placing himself in control of all facets of state power.4 

Barre’s government suffered a serious blow when he launched an unsuccessful military invasion of the ethnic Somali Ogaden region of Ethiopia in 1977. Barre’s invasion accelerated the Soviet Union’s decision to support the Marxist Ethiopian regime and to abandon support for Somalia, leading to a military defeat for Barre in 1978. This set in motion an economic and political crisis of legitimacy that ultimately led to the collapse of the Barre dictatorship.5 After breaking with the Soviet Union,6 Barre abandoned “scientific socialism,” allied himself with the West, and sought refuge increasingly in the support of his Darod clan.7

The increasing clan basis of Barre’s regime led to the formation of opposition fronts that were similarly clan-focused, as non-Darod clans felt excluded from power.8 One of the first setbacks to Barre came in 1981 when his attempts to undermine the economic and political power of the Isaaq clan led to the formation of the Isaaq-dominated Somali National Movement (SNM).9 The SNM soon began launching small-scale attacks against government and military posts inside Somalia.  

Barre responded to the SNM with what Human Rights Watch described as “savage counterinsurgency tactics,” ordering massive bombardments of northern towns and villages that killed tens of thousands of Somali civilians and led to the internal displacement of some 500,000 northerners, with another 500,000 seeking refuge in Ethiopia.10

Following his 1978 break with the Soviet Union, Barre had enjoyed substantial support from the West, particularly the United States11—allowing Barre to expand his army from an estimated 3,000 at the time of independence to a “suffocating” 120,000 by 1982.12 Reports from Amnesty International, Human Rights Watch, and the press about the atrocities being committed by the Barre regime led, however, to a sharp reduction in US and western aid by late 1989.

The Fall of the Barre Regime and the Outbreak of Clan Fighting

President Barre was overthrown in January 1991 by a coalition of insurgency movements including the Isaaq-dominated SNM, Gen. Mohamed Farah Aideed’s largely Hawiye clan-based United Somali Congers (USC) fighting in the south-central regions, and the Ogaden clan-dominated Somali Patriotic Movement (SPM) that was based in southern Somalia.13

The removal of the Siad Barre government spurred new conflict among and within the clan-based opposition movements. The USC split into two factions, one supporting General Aideed and a second supporting a Hawiye businessman from the Abgal sub-clan, Ali Mahdi Mohammed. Mohammed was appointed as interim president by a group of politicians and influential elders from the Hawiye clan within two days of Barre’s ouster.14

By late 1991 increasing numbers of individuals and armed groups competed for power in the vacuum left by Siad Barre’s departure. The early 1990s saw some of Mogadishu’s worst fighting as militia mobilized by General Aideed fought with those of Ali Mahdi to impose their control over the capital and the rest of the country.15

The war divided the capital city into two zones separated by a “green line,”16 displaced tens of thousands of people, and cost thousands of civilians in Mogadishu and south-central Somalia their lives. The fighting in Mogadishu and subsequent clan-based conflict further south also severely affected the local harvest, creating an unprecedented famine in fertile southern Somalia.17 Humanitarian organizations estimated that between February 1991 and December 1992, 300,000 people may have lost their lives.18

Between 1991 and 1993, as people died of starvation and related illnesses in their tens of thousands, freelance and clan-based militia obstructed aid efforts and looted relief. A 1992 United Nations (UN)-negotiated ceasefire failed and prompted the first UN military intervention to protect relief access and aid workers—the operation known as the United Nations Operation for Somalia (UNOSOM). In December 1992 UNOSOM’s failure to end the fighting led the United States to overcome its initial reluctance and to send troops, under US command, to the UN Task Force on Somalia (known as UNITAF and codenamed “Operation Restore Hope”). In May 1993 UNOSOM and UNITAF were replaced by UNOSOM II, which had a more robust mandate under Chapter VII of the UN Charter and more than 30,000 troops from various countries.19 US troops withdrew in 1994 after they became embroiled in conflict with General Aideed.20 UNOSOM II left Somalia in March 1995 without achieving a breakthrough towards long-term political stability for Somalia, initially a key objective of the mission.21

The civil war and the successive US and UN military interventions in the early 1990s left several legacies, including a dramatic increase in the number of Somali factions and armed groups (none of which shared any common political platform or national vision), the empowerment of individual warlords, and a deep reluctance on the part of powerful states such as the United States to intervene in Somalia.22

Successive Failed Peace Processes: 1991–2004

Peace initiatives began as early as 1991. After UNOSOM withdrew in 1995, diplomatic responsibility for Somalia was left to regional governments. Egypt, Djibouti, Yemen, Ethiopia, and Kenya took turns hosting peace conferences to end the violence and reestablish a Somali state.23 Of more than a dozen peace conferences, two were noteworthy for an understanding of current events.

The first of these was in May 2000 in Arta, a town in neighboring Djibouti.24 During the negotiations Djibouti tried to create an atmosphere that limited the role and influence of the warlords in the conference, instead emphasizing the role of civil society groups and clan elders. The conference resulted in the first Transitional National Government (TNG) led by Abdulkasim Salad Hassan, a controversial and long-time minister under Siad Barre.25

The Djibouti conference also created a 245-member parliament and approved the appointment of Ali Khalif Gallaydh as prime minister. It set up a power-sharing system based on the so-called 4.5 system—meaning an equal number of representatives for the four major clans and half of a major clan’s share for all the minority clans together.

Key players such as the United States, the European Union, and the African Union (then the Organization of African States, OAS) were hesitant to make any firm commitment to Somalia, given the numerous previous failed peace processes, and provided little support to the TNG.26 But the biggest setback came from local warlords who refused to recognize and collaborate with the new administration and instead formed a Somali Reconciliation and Restoration Council (SRRC) in Ethiopia in 2001 to challenge the legitimacy of the new government.27

By 2002 it was clear the TNG had failed to establish any credible administration and its mandate was running out. It lacked authority on the ground and could not prevail against the opposition of powerful warlords. Kenya offered to host both sides, the TNG and SRRC, for European Commission-financed talks in Eldoret in October 2002. After two years of difficult negotiations, in 2004 Kenya brokered a power-sharing agreement through the Inter-Governmental Authority on Development (IGAD, a regional umbrella group which comprises Ethiopia, Kenya, Djibouti, Sudan, Somalia, Uganda; Eritrea withdrew from membership this year in protest of IGAD’s view on Ethiopia’s role in Somalia).28 The result of this process was the establishment of the current Transitional Federal Institutions: a Transitional Federal Charter, a Transitional Federal Government (TFG) and a Transitional Federal Parliament (TFP) consisting of 275 members.

In October 2004 the TFP elected Abdullahi Yusuf Ahmed, a leading member of the SRRC group, as president of the TFG, who in turn appointed Ali Mohammed Gedi as prime minister.29 Following pressure from Kenya to relocate and establish a government in Somalia, in May 2005 the TFG tried to establish itself within Somalia, but immediately split, with some members moving to Jowhar and some to Baidoa.30

The Ethiopian Factor

Recent events in Somalia are closely linked to regional developments. Ethiopia and Somalia are historically, socially, and politically intertwined, with several episodes of religious and territorial disputes over the Somali region of eastern Ethiopia known as the Ogaden, most recently in 1964 and 1977.31 Ethiopian concerns over continuing Somali nationalist sentiments towards the ethnic Somali Ogaden region remains a key element in Ethiopian foreign policy decision-making. 32

Successive Ethiopian governments have supported Somali opposition leaders and movements and the Ethiopian government led by Prime Minister Meles Zenawi has been closely involved in the various Somali peace processes. Several of the current leading figures in Somalia’s military and political landscape have either received longstanding support from—in the case of Abdullahi Yusuf—or had antagonistic relations with—in the case of Sheikh Hassan Dahir Aweys, a former deputy leader of the militant Islamist group Al-Itihaad Al-Islaami—the Ethiopian government. 

Ethiopian mistrust of Sheikh Aweys stems from his connection to Al-Itihaad Al-Islaami, originally a Salafi religious movement that evolved into a militant Islamist organization. Sheikh Aweys was actively involved in forming Al-Itihaad’s military wing in the early 1990s, which fought against Ethiopia and then-militia leader and current TFG President Abdullahi Yusuf’s faction in Puntland.33 Al-Itihaad was allegedly responsible for several bombings in Ethiopia in the mid-1990s that led to its designation on a US sanctions list of individuals and organizations after the September 11, 2001 attacks.34 In 1998, following Ethiopia’s defeat of Al-Itihaad in southwestern Somalia, Sheikh Aweys returned to Mogadishu and helped found one of the clan-based Islamic Courts.

Ethiopian involvement in Somalia remains a divisive and politically charged issue for Somalis, many of whom view Ethiopian motives in Somalia with deep distrust.35 Some Somalis blame Ethiopia for the inability of the TNG, the predecessor to the current TFG, to establish an enduring government.36

Ethiopian interests in Somalia are also closely linked to Ethiopia’s relations with Eritrea. Although there has been little active fighting since their bloody 1998-2000 border war ended, Eritrea and Ethiopia remain bitter rivals and both governments have engaged in a form of proxy war in Somalia dating back to the late 1990s.37 Eritrea has provided military aid and training to a variety of Ethiopian insurgent groups based in the Ogaden and Somalia, and Ethiopia has supported the TFG.38

The Rise of the Islamic Courts in 2006

In June 2006 the Somali political scene was shaken by the emergence of an alliance of sharia (Islamic law) courts, the Islamic Courts Union (ICU). The ICU, with Sheikh Hassan Dahir Aweys among its leaders, drove the warlords from Mogadishu.39 Although the appearance of the Islamic Courts as a potent political movement was a surprise to many observers, the courts had longstanding roots in Mogadishu.40

In December 2004, just two months after the formation of the TFG, a group of clan-based courts that had been operating in Mogadishu for years joined to launch the ICU.41 Sheikh Sharif Sheikh Ahmed, a schoolteacher from Mogadishu, was appointed chair of the alliance.42 By 2005 there were 11 Islamic Courts from different clans operating in Mogadishu under sharia.43

The increasing influence of the Islamic Courts came against the backdrop of growing US concern over the presence of alleged terrorism suspects in Somalia.44 The US had claimed for several years that several individuals linked to al Qaeda and the 1998 bombing of the US embassies in Kenya and Tanzania were being sheltered by radical Islamists in Mogadishu.45 The US Central Intelligence Agency (CIA) initially tried to capture the individuals by paying warlords in Mogadishu to abduct the men and transfer them to CIA custody. Three of the individuals most wanted by the US were Fazul Abdullah Mohamed, a national of the Comoros Islands, Abu Talha al-Sudani, a Sudanese national, and Saleh Ali Saleh Nabhan, a Kenyan.46

Reports of a growing jihadi network in Somalia strengthened fears that the ICU would encourage Somalia to become a breeding ground for terrorism in the Horn of Africa.47 On February 18, 2006, a few key warlords in Mogadishu formed a new alliance called the Alliance for the Restoration of Peace and Counter-Terrorism (ARPCT), with US backing.48 Its aim was to capture the individuals linked to the east Africa bombings.49

Instead, US support for the notorious warlords who formed the APRCT backfired, generating further popular support for the ICU,50 which extended its territorial control over a large part of central and southern Somalia and ultimately defeated the APRCT in bitter fighting in Mogadishu in June 2006.51

As the ICU fought the US-backed warlords in early 2006, the Transitional Federal Government of Somalia was struggling to establish itself in Somalia.52 It set up temporary bases, initially in Jowhar town and later on in Baidoa, 250 kilometers northwest of Mogadishu, but received little international support.53 It was only when the ICU emerged as a powerful political actor in southern Somalia that regional and international actors turned to the TFG as a more palatable form of Somali leadership.54

Within a matter of four months, between June and October 2006, the ICU was in control of seven of the ten regions in south-central Somalia. The Islamic Courts had restructured into the Council of Somali Islamic Courts (CSIC), with the formation of a consultative council headed by Sheikh Aweys and an executive body headed by Sheikh Sharif Sheikh Ahmed.55 The appointment of Sheikh Aweys as one of the main leaders of the CSIC further alarmed both Ethiopia and the US, which had already placed Sheikh Aweys on a sanctions list in 2001 for his alleged links to terrorism.56

A June 30, 2006 video message from Osama Bin Laden urged Somalis to support the ICU and build an Islamic state, and threatened to fight the US if it intervened in Somalia.57

Nationalist statements from some of the ICU leadership further fuelled Ethiopian fears that the ICU hoped to unite ethnic Somali communities in neighboring northern Kenya and Ethiopia’s Ogaden with Somalia. Ethiopia was also concerned by the potential impact on Ethiopia’s own large Muslim and Somali population of the Islamic Courts’ effort to establish political Islam in Somalia.58

The emergence of the ICU as a military threat in 2006 prompted the Ethiopian government to strengthen its political and military support to the TFG.59 Ethiopia was the primary supplier of arms to the TFG and some individual warlords, but Uganda and Yemen also contributed arms and other supplies.60

On the other side, UN experts monitoring Somalia’s utterly ineffective arms embargo in 2006 documented arms flows and supply of military materiel and training to the Islamic Courts from seven states: Djibouti, Egypt, Eritrea, Iran, Libya, Saudi Arabia, and Syria.61

Following the ICU’s victory over the warlords in June 2006, Ethiopia moved increasing amounts of troops and military materiel into Baidoa, the TFG stronghold, to protect it from any ICU attack.62 The US government supported its ally Ethiopia.63

Peace Talks Fail: June–December 2006

The rise of the Islamic Courts narrowed down the rival groups in Somalia to two: the Transitional Federal Government and the Islamic Courts Union. Appeals for peace talks mounted in an effort to combine the political legitimacy of the TFG and the stability restored to many parts of southern Somalia by the Islamic Courts.

Sudan agreed to host negotiations and on June 22, 2006, the two sides agreed on mutual recognition and further talks in Khartoum. A second round of talks under Arab League auspices in September 2006 made further apparent progress, with agreement on integrated security forces and a commitment to discuss power sharing arrangements. A third round of negotiations was scheduled for October 30, 2006, but was forestalled by Somalia’s first suicide bombing on September 18, an assassination attempt on President Abdullahi Yusuf.64 ICU leaders denied responsibility for the attack.65

Throughout the negotiations both the ICU and the TFG/Ethiopia continued to bolster their military preparations. In the run-up to the third round, the ICU also continued its territorial expansion, taking the strategic southern town of Kismayo in late September 2006, allegedly with a coalition of forces including advisors from Eritrea and fighters from the Ogaden National Liberation Front (ONLF) and the Oromo Liberation Front (OLF).66

The TFG, Ethiopia, and international government backers viewed this development with alarm, interpreting it as a prelude to an ICU attack on Baidoa, the only TFG stronghold in south-central Somalia. The Ethiopian military moved to bolster its presence not only in Baidoa, but also in Puntland and other areas of Somalia.67

By the time the third round of talks began in Khartoum in October 2006, the situation was at an impasse. The ICU insisted that Ethiopian troops leave Somalia and that IGAD should not have a mediating role in the talks. The TFG took the opposite position, calling for IGAD involvement and the ICU’s withdrawal from recently captured areas. The talks ended in deadlock and Somalia entered a new round of hostility.68

The Fall of the Islamic Courts

November and December saw rising tensions between the ICU and the TFG/Ethiopians and increasing military preparations on the ground by both sides.69 The UN Security Council on December 6 passed resolution 1725 authorizing a regional military intervention in Somalia, a development long desired by the TFG. The US-led resolution did little to reduce the tensions and in fact may have increased them.70 Although the final resolution specified that troops from bordering countries should not be included in IGASOM, the proposed IGAD deployment in Somalia, it made no mention of the existing Ethiopian presence in Somalia and contained enough elements to be viewed as pro-TFG by the Islamic Courts and independent analysts.71

The ICU saw the Security Council resolution as blatant support for the Ethiopian presence. On December 12, 2006, the ICU’s defense chief, Sheikh Yusuf Mohamed Siyad Indha’adde, gave the Ethiopian military in Somalia a week to withdraw or face forcible expulsion.72 The day after the deadline passed, December 20, fighting started around Baidoa. Although the Ethiopian military were actively defending the town, they denied involvement for several days and only publicly acknowledged their role four days later.73

Ethiopian and TFG forces went on the offensive (TFG militia included forces from Puntland—the President’s home region, the Sa’ad subclan of the Hawiye, and Rahanweyn clan militias) and quickly drove the ICU from Mogadishu and its other urban positions.74 The resistance apparently dissolved after several battles south and east of Baidoa and in the central regions of Somalia just south of Galkayo town. Hundreds of Islamic Courts militia members and some foreign fighters who supported what they viewed as jihad75 reportedly died under Ethiopia’s superior firepower, particularly its aerial capacity.76

The Islamic Courts leadership left Mogadishu on December 26 as the Ethiopian forces advanced on the capital, moving south towards Kismayo and the Juba Valley while many of their Somali supporters merged back into the civilian population.77 Kismayo fell to the Ethiopians on January 1, 2007, forcing the Islamic Courts leadership and supporters further south. The outflux included dozens of foreigners who supported the Islamic Courts, some of whom had been living in Mogadishu with their wives and children.78 Fazul Mohammed and several other individuals on the US wanted list were apparently among the exodus from Mogadishu.79

The US became overtly involved in the military campaign when it launched several airstrikes from AC-130 gunships in southern Somalia on January 7 and 8,80 apparently targeting these fleeing individuals, and sent a limited number of special forces across the border.81 The US had previously made cautious public statements supporting the Ethiopian offensive, but left the military ground operations to its Ethiopian ally. In mid- and late January, Ethiopian, US, and Kenyan security forces cooperated in a coordinated pincer operation. While Ethiopian troops pushed the fleeing Islamists and their supporters towards Ras Kamboni, at the very tip of Somalia on the Kenyan border, US navy ships positioned off the Somali coast cut off potential escapes by sea across the Gulf of Aden.82

As hundreds of people fleeing the conflict arrived at border crossings or in Kenya, Kenyan security forces closed the border and arrested dozens of Somali and foreigners suspected of affiliation with the Islamic Courts or with men wanted by the US (see above).83

Meanwhile, as the Ethiopian and US forces pursued supporters of the Islamic Courts south towards Kismayo, other Ethiopian units and TFG forces settled into military bases and buildings in Mogadishu in the first days of January 2007. These sites included strategic locations such as the new seaport, the airport, Somalia’s former Presidential Palace (also known as Villa Somalia), and other strategic buildings including the former Ministry of Defense and the former headquarters of the Custodial Corps.84 The Ethiopian military also occupied three former Somali military bases situated on the two main highways that link Mogadishu to the southern and central regions.85

1 Maj.-Gen. Mohamed Siad Barre took power in a bloodless coup in October 1969, six days after the assassination of President Abdurashid Ali Sharmarke. For further description and analysis of Somalia’s troubled history, see I.M. Lewis, A Modern History of the Somali: Nation and State in the Horn of Africa (Athens, OH: Ohio University Press, 2003); and Lee V. Cassanelli, The Shaping of Somali Society: Reconstructing the History of a Pastoral People, 1600-1900 (Philadelphia: University of Pennsylvania Press, 1982). See also Ismail I. Ahmed and Reginald Herbold Green, “The heritage of war and state collapse in Somalia and Somaliland: local-level effects, external interventions and reconstruction,” Third World Quarterly 1999, (accessed August 2, 2007).

2 Catherine Besteman, Unraveling Somalia: Race, Violence, and the Legacy of Slavery (Philadelphia: University of Pennsylvania Press, 1999), p. 12.

3 Lewis, A Modern History of the Somali, pp. 209-210.

4 Ibid., pp. 211-212; Amnesty International, “Somalia: Report on an Amnesty International Visit and Current Human Rights Concerns,” AI Index: AFR 52/01/90, 1990.

5 See Maria H. Brons, Society, Security, Sovereignty and the State in Somalia: From Statelessness to Statelessness? (Utrecht, Netherlands: International Books, 2001); Ali Jimale Ahmed, The Invention of Somalia (Trenton, NJ: Red Sea Press, 1995); Ahmed I. Samatar, The Somali Challenge: From Catastrophe to Renewal? (Boulder, CO: Lynne Rienner Publishers, 1994); I.M. Lewis, Blood and Bone: The Call of Kinship in Somali Society (Trenton, NJ: Red Sea Press, 1997).

6 President Barre reacted angrily to the Soviet refusal to support Somalia’s invasion of the Ogaden region and the ensuing war with Ethiopia. All Soviet military experts and diplomatic representatives were expelled from Somalia and Somalia switched policy towards the West. For further analysis, see Ahmed I. Samatar, Socialist Somalia: Rhetoric and Reality (London: Zed Books, 1988); and David A. Korn, Ethiopia, the United States and the Soviet Union (Carbondale, IL: Southern Illinois University Press, 1988).

7 Lewis, A Modern History of the Somali, p. 222.

8 One of the first of these opposition movements was the Somali Salvation Democratic Front (SSDF), led by then-Colonel and current President Abdullahi Yusuf after he survived a failed coup attempt against Siad Barre and fled to Ethiopia in 1978. See Daniel Compagnon, “The Somali Opposition Fronts,” Horn of Africa, vol. 13, no. 1 & 2, April-June 1990, pp. 29-54. 

9 Lewis, A Modern History of the Somali, p. 252.

10 In 1988 Somalia and Ethiopia signed a peace agreement. The SNM feared the loss of its bases in Ethiopia and attacked and briefly captured Hargeysa and Burco. The Barre government bombarded Hargeysa and Burco in reprisal. See Human Rights Watch, “Human Rights in Selected African Countries,” remarks prepared for the House Subcommittee on Foreign Operations by Holly Burkhalter, February 7, 1989; Robert Gersony, “Why Somalis Flee: Conflict in Northern Somalia,” Cultural Survival Quarterly, 13(4), 1989; I.M. Lewis, “The Ogaden and the Fragility of Somali Segmentary Nationalism,” African Affairs, vol. 88, no.353 (1989), pp. 573-579.

11 Jeffrey Lefebvre, Arms for the Horn: U.S. Security Policy in Ethiopia and Somalia, 1953-1991 (Pittsburgh: University of Pittsburgh Press, 1991), p. 14.

12 Hussein M. Adam, “Somalia: A Terrible Beauty Being Born?” in I. William Zartman, ed., Collapsed States: The Disintegration and Restoration of Legitimate Authority (Boulder, CO: Lynne Rienner, 1995), p. 71.

13 Jack L. Davies, “The liberation movements of Somalia,”, August 27, 1994, (accessed July 6, 2007).

14 “Reaction to USC Presidential appointment noted,” BBC World Service London (in English), January 30, 1991, 17:09 hrs GMT, transcript reproduced at (accessed July 27, 2007).

15 Africa Watch (now Human Rights Watch/Africa) and Physicians for Human Rights, No Mercy in Mogadishu: The Human Cost of the Conflict & The Struggle for Relief, March 26, 1992,

16 Jane Perlez, “Airlift to Somalia's Capital Begins As Strife Between Clans Continues,” New York Times, December 21, 1991, (accessed July 3, 2007); Peter Biles, “Africa’s new hell chokes in despair,” Observer (London), January 5, 1992, reproduced at (accessed July 3, 2007).

17 “U.N. Urges Warlords to Open Somali Port,” New York Times, November 22, 1992, (accessed July 3, 2007).

18 “1992: American marines land in Somalia,” BBC News Online, December 9, 1992, (accessed July 3, 2007).

19 Human Rights Watch/Africa, Somalia Faces the Future: Human Rights in a Fragmented Society, vol. 7, no. 2, April 1995.

20 Ibid.

21 Ibid. See also John L. Hirsch and Robert B. Oakley, Somalia and Operation Restore Hope (Washington DC: United States Institute of Peace Press, 1995).

22 The six factions that existed just after Siad Barre left power fragmented into dozens of other factions and splinter groups each vying for power and national resources. See Alex de Waal, Social Science Research Council, “Class and Power in a Stateless Somalia,” February 20, 2007, (accessed July 3, 2007).

23 Ethiopia hosted four peace conferences, Kenya and Djibouti each hosted three, while Egypt, Yemen and Libya hosted one conference each. These conferences sometimes undermined each other. US State Department, “Background Note: Somalia,” May 2007, (accessed August 3, 2007); Ibrahim H. Gagale, “The only Road to Peace in Somalia,” February 8, 2007, (accessed August 3, 2007).

24 “Somali National Peace Conference,” IRINnews, July 4, 2000, (accessed July 4, 2007).

25 “Hero’s welcome for Somali President,” BBC News Online, October 14, 2000, (accessed July 4, 2007).

26 The UN did support the TNG, however, and a TNG representative occupied Somalia’s seat at the UN, which had been vacant since 1991. Andre le Sage, Centre for Humanitarian Dialogue, “Stateless Justice in Somalia Formal and Informal Rule of Law Initiatives,” July 2005, (accessed August 1, 2007).

27 “Somali warlords form unity council,” BBC News Online, March 22, 2001, (accessed July 4, 2007).

28 For analysis of the negotiations see Ken Opala, “Foreign Powers Stalk Somali Peace Talks,” Nation (Kenya), July 21, 2003, reproduced at (accessed July 4, 2007); Zablon Odhiambo and Neddy Mbori, “Somalia: EU backs Igad on peace process,” East African Standard (Kenya), July 19, 2003, reproduced at (accessed July 4, 2007); “SOMALIA: IGAD ministers meet in bid to kick-start Somali peace process,” IRINnews, May 21, 2004, (accessed July 4, 2007); “Somali warlords make peace,” BBC News Online, January 29, 2004, (accessed July 4, 2007).

29 Prime Minister Ali Mohammed Gedi is a former veterinarian who had little political experience when he was appointed to the position. President Abdullahi Yusuf is a former warlord whose relations with Ethiopia started in 1978 during the Derg regime, when Abdullahi Yusuf and other former Somali army officers orchestrated a failed coup to unseat Siad Barre. When Barre executed most of the officers who planned the coup, Yusuf escaped to Ethiopia and helped create one of the first rebel groups based in Ethiopia, the SSDF (see footnote 8). Yusuf was later detained by the Derg government after a difference of opinions, but he was released by Meles Zenawi after Zenawi took power in Ethiopia in May 1991. For further analysis see Mohammed Adow, “Why Ethiopia is on war footing,” BBC News Online, July 21, 2006, (accessed August 2, 2007).

30 International Crisis Group, “Can the Somalia Crisis be Contained?” Africa Report No. 116, August 10, 2006, p. 4.

31 Peter Woodward, The Horn of Africa: Politics and International Relations, (London, New York: Tauris Academic Studies, 1996); David D. Laitin and Said S. Samatar, Somalia: Nation in Search of a State, (Boulder, Colorado: Westview Press, 1987). For a brief timeline on the historical events, see “Timeline: Ethiopia and Somalia,” BBC News Online, January 25, 2007, (accessed July 4, 2007).

32 Somali nationalism stems from the 19th century “scramble for Africa” by the European powers. The northern regions of Somalia came under the protectorate of Britain in 1884–1886. Between 1889 and 1905, the Italian government established its control over the southern regions. In 1896 France claimed Somalia’s red sea coast region and named it French Somaliland (later to become Djibouti after independence in 1977). These three regions plus the northeastern region of Kenya (named the Northern District Frontier by the British), and the western Somali region known as the Ogaden or Region 5 in eastern Ethiopia constitute “Greater Somalia.” In 1960 two of these five regions joined to make the first Somali republic. But Somalia’s first post-independence president, Aden Abdulle Osman (Aden Adde) asserted that Somalis must get the “missing regions” through peaceful means no matter how long it takes.

33 There is debate among analysts about the extent to which Al-Itihaad remained a potent force after its defeat by Abdullahi Yusuf and Ethiopian forces in the 1990s. For analysis of Sheikh Aweys and the origins of Al-Itihaad Al-Islaami see International Crisis Group, “Counter-Terrorism in Somalia: Losing Hearts and Minds?” Africa Report No. 95, July 11, 2005; “Somalia’s Islamists,” Africa Report No. 100, December 12, 2005; and “Can the Somali Crisis Be Contained?” See also André Le Sage, “Prospects for Al Itihad and Islamist Radicalism in Somalia,” Review of African Political Economy, vol. 27, no. 89, September 2001.

34 Al-Itihaad was placed on a US list of organizations designated for asset freezes on September 23, 2001. Sheikh Aweys was named on the same US list on November 7, 2001. See US Department of the Treasury, Office of Foreign Assets Control, “Executive Order 13224—Blocking Property and Prohibiting Transactions with Persons who Commit, Threaten to Commit, or Support Terrorism,” (accessed August 1, 2007).

35 Abdirahman Aynte, “Somalis Decry Ethiopian Invasion, U.S. Support,”, January 8, 2007, (accessed August 2, 2007);
Stephanie McCrummen, “Ethiopia Steps Up Attacks on Somalia,” Washington Post, December 26, 2006, (accessed July 4, 2007); and Martin Fletcher, “We don’t have civil servants. We have guns,” Times (London), April 27, 2007, (accessed July 4, 2007).

36 See United Nations Security Council, Report of the Secretary-General on the situation in Somalia, S/2002/709, June 27, 2002, p. 4, (accessed August 1, 2007).

37 In “Avoiding Conflict in the Horn of Africa,” published by the Council on Foreign Relations, regional analyst Terrence Lyons argued that the breakdown of the Eritrea-Ethiopia peace implementation process precipitated the intervention of both countries in neighboring Somalia. Eritrea’s policy of supporting the ICU and rebel groups fighting inside Ethiopia—such as the Ogaden National Liberation Front (ONLF) and the Oromo Liberation Front (OLF)—escalated in 2006. These rebel groups are led by Gen. Mohammed Omar and Dawud Ibsa respectively and both men are currently based in Eritrea. Terrence Lyons, Council on Foreign Relations, “Avoiding Conflict in the Horn of Africa,” December 2006, (accessed August 5, 2007). For further analysis see Abdul Mohammed, Social Science Research Council, “Ethiopia’s Strategic Dilemma in the Horn of Africa,” February 20, 2007, (accessed July 4, 2007).

38 For a detailed description of Eritrean military support to the ICU and Ethiopian military support to the TFG in early 2006, see United Nations Security Council, Report of the Monitoring Group on Somalia pursuant to Security Council resolution 1676 (2006), S/2006/913, November 22, 2006, pp. 11-21.

39 Sheikh Aweys took a leading role in the rise of the ICU and became chair of the ICU’s consultative council in mid-2006. After the fall of the courts in December 2006, he apparently fled Mogadishu and is currently thought to be in Asmara, Eritrea.

40 The establishment of Islamic courts in Mogadishu began in 1994, while UNOSOM II was still present in Somalia, and quickly received popular support from a population exhausted by years of lawlessness and violence at the hands of numerous corrupt warlords. The main aim of the courts was to tackle pervasive crime in Mogadishu. As the courts expanded, they drew the attention of north Mogadishu’s then-political leader, Ali Mahdi Mohammed, who feared that the courts’ growing support base could diminish his power. In 1996 he cracked down on the courts in north Mogadishu, but popular support for the Courts continued. In 1998, with the support of the business community, two of the clans in south Mogadishu set up Islamic courts to curb banditry and murders within their own clans. US State Department, “Somalia: Country Reports on Human Rights Practices,” Bureau of Democracy, Human Rights, and Labor, February 23, 2001, (accessed August 2, 2007).

41 Ken Menkhaus, “There and back again in Somalia,” Middle East Report Online, February 11, 2007, (accessed July 5, 2007).

42 Asad Mohamed, “Who is the most powerful man in Mogadishu?” (Waa kuma ninka uku awooda badan magaalada Muqadisho), Radio Dalmar, June 13, 2007, (accessed March 28, 2007).

43 International Crisis Group, “Can the Somali crisis be contained?”p. 10.

44 James Phillips, “Somalia and Al-Qaeda: Implications for the War on Terror,” Heritage Foundation, April 5, 2002, (accessed July 11, 2007); International Crisis Group, “Counter-Terrorism in Somalia”; United Nations Security Council, Report of the Monitoring Group on Somalia pursuant to Security Council resolution 1558 (2004), S/2005/153, March 8, 2005.

45 US State Department, Office of the Coordinator for Counterterrorism, Country Reports on Terrorism 2004, April 27, 2005, (accessed August 1, 2007).

46 International Crisis Group, “Counter-Terrorism in Somalia,” p. 8. All three individuals are on US sanctions lists for their alleged affiliation to terrorist activity, along with several Somalis, including Sheikh Aweys and Hassan Al-Turki.

47 “A state of utter failure—Somalia,” Economist, December 17, 2005.

48 The Somali warlords behind the formation of the ARPCT were members of the TFG. They included Muse Sudi Yalahow (trade minister), Mohammed Qanyare Afrah (security minister), Botan Issa Alim (disarmament minister), and Omar Mohammed Finish (religious affairs minister), as well as several business and other militia leaders.

49 “Avoid Kenya, US warns,” BBC News Online, May 15, 2003, (accessed July 3, 2007).

50 “US secretly backing Somali warlords,” Washington Post, May 18, 2006; C. Bryson Hull, “U.S. moves diplomat critical of Somali warlord aid,” Reuters, May 30, 2006; Antony Barnett and Patrick Smith, “US accused of covert operations in Somalia,” The Observer, September 10, 2006.

51 “Islamists claim Mogadishu victory,” BBC News Online, May 5, 2006, (accessed July 3, 2007); Xan Rice, Oliver Burkeman, and Rory Carroll, “US policy in Somalia unravels as Mogadishu falls,” The Irish Times, June 10, 2006. For further analysis see Roland Marchal, Social Science Research Council, “Somalia: A new front against terrorism,” February 5, 2007, (accessed August 1, 2007).

52 “US urges Somali unity in rare personal appeals to warlords,” Agence France-Presse, January 27, 2006.

53 “Somalia: TFG preparing to begin operating from Jowhar,” IRINnews, June 22, 2005, (accessed July 14, 2007).

54 Rob Crilly, “Somalia’s transitional government on the verge of collapse,” Christian Science Monitor, August 4, 2006.

55 “Formation of Islamic Courts Council Announced” (Gole kulmiya maxkamadaha Somaliya oo lagu dhawaaqay [Magacyada Golaha shuurada & kan fulinta]), Goobjood, June 25, 2006, (accessed July 11, 2007); “SOMALIA: Islamic courts set up consultative council,” IRINnews, June 26, 2006, reproduced at (accessed July 11, 2007).

56 Marc Lacey, “Somalis present a militant face: new leader seen as terrorist by U.S.,” International Herald Tribune, June 27, 2006.

57 “Bin Laden releases Web message on Iraq, Somalia,” USA Today, July 1, 2006, (accessed August 1, 2007).

58 International Crisis Group, “Counter-Terrorism in Somalia.” See also Tom Allard, “Terrorists look to Somalia as an emerging safe haven,” Sydney Morning Herald, November 4, 2006.

59 Both the ICU and the TFG received substantial military support and supplies from regional and other states, as well as independent arms trading networks. The UN Security Council imposed an arms embargo on Somalia in 1992, but the embargo has been repeatedly violated. For further details on the arms flows and military build up in 2006, see United Nations Security Council, Report of the Monitoring Group on Somalia pursuant to Security Council resolution 1676 (S/2006/913), November 22, 2006, and previous reports by the UN Monitoring Group, (accessed July 14, 2007).

60 United Nations Security Council, Report of the Monitoring Group on Somalia pursuant to Security Council resolution 1676 (S/2006/913), November 22, 2006, pp. 27-29.

61 Ibid., pp. 10-16, 21-25. Much of the UN report was viewed by independent experts and analysts as largely credible, with the exception of allegations of ICU support and cooperation with Hezbollah and allegations that Iran attempted to trade arms for Somali uranium. Confidential email communication from correspondent (name withheld) to Human Rights Watch, November 21, 2006. See also Andrew McGregor, “Accuracy of New UN Report Doubtful,” Global Terrorism Analysis, The Jamestown Foundation, vol. 3, no. 45, November 21, 2006, (accessed July 14, 2007).

62 Ibid., p. 17.

63A confidential UN cable obtained by Human Rights Watch indicates that in a conversation with UN officials in June 2006, US Assistant Secretary of State Jendayi Frazer noted that the situation in Somalia was “uncertain.” According to the notes, she presented the view that Eritrea had stepped over the line and that Ethiopia viewed Eritrean action in Somalia “as tantamount to opening a second front against Ethiopia.” Dr. Frazer’s best-case scenario was that the ICU and TFG would engage in dialogue; the worst-case scenario was the expansion of the ICU throughout Somalia and the disintegration of the TFG. Dr. Frazer noted that the latter scenario would have a major negative impact in the Horn and that the US and IGAD would not allow it. She allegedly expressed the view that while the US feared an Ethiopian intervention could rally “foreign elements,” the US would rally with Ethiopia if the “Jihadists” took over. Document on file with Human Rights Watch.

64 “Somali government forms panel to probe suicide bombing,” Agence France-Presse, September 20, 2007.

65 “Somali car ban to stop bombers,” BBC News Online, December 4, 2006, (accessed July 17, 2007).

66 “Somalia: Protests after Islamic courts take Kismayo,” IRINnews, September 25, 2006, (accessed July 14, 2007). See also United Nations Security Council, Report of the Monitoring Group on Somalia pursuant to Security Council resolution 1676 (2006), p. 41.

67 Ethiopia may have also been concerned by the apparently strengthening links between Eritrea, the ICU, and the Ethiopian insurgencies. United Nations Security Council, Report of the Monitoring Group on Somalia pursuant to Security Council resolution 1676 (2006), pp. 17-19.

68 Ali Musa Abdi, “War fears mount after peace talks collapse,” Agence France-Presse, November 2, 2007, reproduced at,21985,20687412-5005961,00.html (accessed July 3, 2007).

69 Mark Tran, “Looming Somali war menaces whole region,” Guardian (London), December 14, 2006,,,1972298,00.html (accessed August 1, 2007).

70 “Security council approves African protection, training mission in Somalia,” UN Security Council news release, December 6, 2006, (accessed July 4, 2007). For a critical analysis of the resolution see Matt Bryden, “Storm Clouds over Somalia as Rivals Prepare for Battle,” Nation, December 8, 2006.

71 Resolution 1725 mandated the mission to monitor progress by the Transitional Federal Institutions and the Islamic Courts Union in implementing agreements reached in their dialogue, to ensure the free movement and safe passage of all involved with the dialogue process, and to maintain and monitor security in Baidoa. United Nations Security Council, Resolution 1725, S/RES/1725 (2006), December 6, 2006, (accessed August 1, 2007).

72 Sahal Abdulle, “Somali Islamists give ultimatum to Ethiopia,” Reuters, December 12, 2006, reproduced at (accessed July 5, 2007).

73 Aweys Osman Yusuf, “Ethiopia Denies its Troops were involved in Somalia’s clashes,” Shabelle Media Network, December 21, 2006; “Somali fighting escalates as Ethiopia deploys tanks: residents,” Agence France-Presse, December 21, 2006; “Ethiopia Forced into War against Somali Islamists-PM,” Reuters, December 24, 2006.

74 “Somali Islamists retreat from positions after withering attacks,” Agence France-Presse, December 26, 2006.

75 Aweys Osman Yusuf, “Islamists Call World Muslim Fighters to Wage Their Jihad in Somalia,” Shabelle Media Network, December 23, 2006; “Somalia Islamists suffer heavy casualties,” Associated Press, December 26, 2006, reproduced at (accessed July 5, 2007).

76 Human Rights Watch interviews with eyewitnesses, diplomats, media, and others (names and locations withheld), February 2007.  

77 “Islamists abandon Somali capital,” BBC News Online, December 28, 2006, (accessed July 5, 2007). For analysis on the defeat of the Islamic Courts, see International Crisis Group, “Somalia: The Tough Part Is Ahead,” Africa Briefing No. 45, January 26, 2007. See also Dr. Abdishakur Jowhar, “A war of miscalculation,”, December 2006, (accessed July 5, 2007); and “Islamic leader vows to keep fighting for control of Somalia,” Associated Press, December 29, 2006, reproduced at (accessed July 5, 2007).

78 Mike Pflanz, “US hunts Al-Qaeda suspects fleeing Somalia,” Daily Telegraph (London), January 5, 2007, (accessed July 5, 2007). For a description of the individuals wanted by the US and an analysis of US counter-terrorism policy in Somalia, see International Crisis Group, “Counter-Terrorism in Somalia,” pp. 9-11.

79 Human Rights Watch interviews with eyewitnesses (names and locations withheld), February and April 2007.

80 Jim Garamone, “Aircraft Attack Al Qaeda Haven, Ike Moves off Somalia Haven,” American Forces Press Service, January 9, 2007, (accessed August 1, 2007). James Gordon Meek, “US Targets Al Qaeda Bigs in Somalia,” New York Daily News, January 10, 2007; “US airstrikes in Somalia target embassy bombers,” Independent (London), January 9, 2007, (accessed August 1, 2007).

81 An eyewitness told Human Rights Watch that US agents interrogated captured suspects in this period in Kismayo and Ras Kamboni. Human Rights Watch telephone interview, July 17, 2007. A Pentagon spokesperson initially claimed the attacks targeted the “principal al-Qaeda leadership in the region” but later acknowledged that the strikes had missed their intended targets. Jim Garamone, “Aircraft Attack Al Qaeda Haven, Ike Moves off Somalia Haven”; Andrew England, “Somalia air strike ‘missed Al Qaeda leaders,’” Financial Times, January 12, 2007. Instead, dozens of villagers and hundreds of animals were allegedly killed in air strikes in that period, although whether responsibility lay with the US or with Ethiopian aircraft remains unclear. “Somali elders say about 100 killed in US, Ethiopian airstrikes,” Agence France-Presse, January 11, 2007; “At least 70 people killed in Somali aerial attacks: Oxfam,” Agence France-Presse, January 12, 2007.

82 “US deploys forces to capture fleeing Somali Islamists,” Agence France-Presse, January 3, 2007; Chris Tomlinson, “Target of U.S. Air Strike Wanted by FBI,” Associated Press, January 9, 2007. Human Rights Watch interviews in Nairobi, February 2007. US warships off the coast launched further strikes in Puntland, northern Somalia, on June 1, 2007. Mahad Elmi and Shashank Bengali, “US warship targets suspected militants in Somalia,” McClatchy, June 2, 2007, (accessed August 5, 2007).

83 “Kenya captures Islamists Fleeing Somalia,” United Press International reproduced in World Peace Herald, January 3, 2007, (accessed August 1, 2007). Among the people detained in Kenya were more than 30 women and children of numerous nationalities, including the family of Fazul Mohammed, a man on the US wanted list. After weeks and months in detention in Nairobi prisons, where many were interrogated by US and British security agents, at least 85 people were expelled to Somalia and then transferred to Ethiopia, where many are still in incommunicado detention. Daniel Maldonado, a US citizen, was rendered from Kenya to the US for prosecution in federal court. “US: Stop the Guantanamo Circus,” Human Rights Watch news release, March 27, 2007,  In June the US Department of Defense announced that another detainee, Mohammed Abdulmalik, had been rendered to Guantanamo several days after he was reportedly arrested. “Terror Suspect Transferred to Guantanamo,” Department of Defense news release, June 6, 2007, (accessed August 5, 2007). At least 25 women and children were deported from Kenya to Somalia in January and February, some of whom were the subject of pending habeas corpus applications in the Kenyan courts. See “Somalia: People Fleeing Somalia War Secretly Detained,” Human Rights Watch news release, March 30, 2007, For further detail see Letter from Human Rights Watch to Kenyan Director of Political Affairs Thomas Amolo, March 22, 2007,

84 The headquarters of Somalia’s Custodial Corps (Prison Services) is close to a number of key roads that go to the sea and airport and lies on the main highway that leaves the capital towards Baidoa, Kismayo, and the southern regions of the country.    

85 The bases are Arbiska, on Afgoi road, and El-Irfid and Maslah Barracks, situated on Bal'ad road.