The fight against terrorism in the Arab world has been going on for many decades. Algeria and Egypt are at the forefront of that struggle. Their armed forces, police and intelligence agencies have accumulated vast experience in counter-terrorism operations. But the price that Algerians and Egyptians paid for that experience is high. In the 1990s, Algeria and Egypt lived through a “black decade”. Radical Islamist movements in Algeria and Egypt openly challenged the state, starting a civil war (in Algeria) and unleashing mass terror against law enforcement officers and tourists (in Egypt). The head of Algeria, Mohamed Boudiaf, fell at the hands of Islamists, Egyptian President Husni Mubarak almost died in an assassination attempt, and tens of thousands of people became victims of attacks by Islamic extremists. The bloody battle with Islamic extremist armed groups in Algeria and Egypt ultimately formed    the modern anti-terrorist security system in those countries. The present article will discuss causes of the most acute crises in the sphere of internal security in Algeria and Egypt at the end of the twentieth century, the characteristics of the actions of armed radical Islamist groups and a comparative analysis of the security policies of the Algerian and Egyptian governments.