At present ethnic separatism is shown in various regions practically on all continents and it is the same serious call of the international stability and safety, as religious extremism and drugs. Ethnic separatism is shown and in the Southern Asia, particularly, in India, Pakistan, Sri - Lanka, leading to terrorism acts and a numerous death. The author analyzes sources and the reasons of ethnic separatism in Pakistan. Author marks that the basis for statehood of Pakistan while independence declaration was not ethnic, but cultural and religious factors, which already contained potential separatism. Article tells us about modern manifestation of ethnic separatism in Pakistan. In particular, the author describes sources, the reasons and manifestations of separatism of Pushtuns and Beludzhy. According to the author, separatism of Beludzhy and Pushtuns is the specific danger not only to integrity of Pakistan. This can lead in the long term to disintegration of the state that is fraught with serious consequences for stability and safety not only for the Southern Asia, but also for other regions nearby Russia.