The 1998 U.S. Embassy bombings in Nairobi, Kenya, and Dar es Salaam, Tanzania, sparked fear that Muslim Somalia's failed state would provide safe haven to East African terrorists—and breed new ones. The Pentagon believes the embassy bombers have been using Somalia as an intermittent hideout. Two radical Islamist militias have been born in Somalia since the 1980s, although their ambitions have been limited to the Horn of Africa.

The U.S. military has had a hard time monitoring Somalia. After the failed "Black Hawk Down" intervention in 1993, the Pentagon decided to keep U.S. forces out of the country. A military official at the Pentagon says they learned how quickly Somalis would unite against any U.S. presence in their country. "Any armed foreign forces are viewed as enemies. As soon as a Somali sees one of our guys, that's it." The U.S. military has several encampments along the Kenyan side of Somalia's border. In neighboring Djibouti, there is a U.S. base focused on regional counterterrorism, the Combined Joint Task Force—Horn of Africa, which was set up in 2002.