Somalia has engendered the policy debate on the extent of the spread of transnational Islamist Jihadist groups in the Horn of Africa (HOA) and their consequences for peace and security across the region. These concerns are justified given the emergence since the late 1980s of extremist groups such as the Eritrean Islamic Jihad Movement and the Somali Jihadist Islamist groups of the likes of Al-Ittihad, the Islamic Courts Union and currently Al Shabab. The leaders and fighters of these groups relocated to the HOA after the defeat of the Taliban following the 2001 US invasion of Afghanistan. The operations of these transnational Islamist groups within and across the countries of the Horn pose serious challenges to the region and beyond.