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Following the seminal events of 11 September 2001, and especially since 12 October 2002, southeast Asia has come into focus as the so-called ‘second front’ in the war against international terrorism. However, the threat of terrorism to southeast Asia emanating from radical Islam predated these events. An emerging security concern in recent years has been the rise of extreme Islamic groups. In addition, there exist Islamic separatist/guerilla groups within the region which envision separate Islamic states, and which have been actively engaged in long-running insurgencies against the central governments in the region. In evaluating the nature of the threat emanating from militant Islamic terrorism, there is a need for better typologies to explain the complexity of home-grown Muslim militant groups, and the emergence of transnational linkages both among them and with international Islamic terrorism. These complexities, coupled with the presence of fundamental grievances which long predated 11 September 2001, point to the necessity for a more broad-based strategy that takes into account the presence of fundamental grievances. But the varied nature of these grievances, and the difficulties that have been encountered in meeting the challenges posed by militant Islam, mean that the war against terrorism will be long drawn-out. Containment, not victory, will be the most realistic outcome.