The issue of spreading of radical Islam in East Africa is one of the most important in region's development trends studies. In this regard, it is quite important to study the genesis, ideological and social background of the most active Islamist groups. Somalia plays key role in this process in East Africa. The spread of radical fundamental ideology in this country was determined by several factors such as specific mentality and social values of Somalia tribes, clan structure of the society, total impoverishment of the population, bloody wars and actual disintegration of the country in the beginning of 1990s. In these conditions, the unification of the country was based on traditional Islamic structures. First, people tired of chaos spontaneously united around Islamic courts that became centers of power. Then other state institutes united around them and as a result, the Islamic Courts Union (ICU) was formed. ICU started to control most of the country. Further, other moderate Islamic groups started to spread their influence. Among them such groups as Ahl al-sunna wa al-djama'a and Raskamboni movement, often connected with the activities of Somalia Sufis, and radical organization al-Shabaab should be mentioned. After 2011, we can witness the process of radicalization when politically active movement is turning into terrorist organization, which has spread its influence on other countries of East Africa. Having connections with radical Islamists in Yemen, Afganistan, Pakistan and Saudi Arabia al-Shabaab united with al-Qaeda in 2012. Fundamental organizations of the region (mostly Somalia) are not homogeneous, they provide spectrum of very different religious, political, cultural views, aspirations and moods of various social strata, ethnic and clan groups. The source base of the research includes mass media materials, analytical articles and reviews in English, French and Russian. The analysis of scientific articles and monographs about the radical Islamism in Northern, West and East Africa also lays in basis of this research.