The emergence of violent Muslim vigilante groups in regions of Indonesia where there has been serious inter-religious conflict is one of the most conspicuous new phenomena in contemporary Indonesian Islam. During the brief presidency of Abdurrahman Wahid, such groups often gained control of the streets, and the army and police appeared unable, or unwilling, to contain them. Most observers of modern Indonesia agree that much of the violence is financed by military and civilian interest groups, and is provoked by struggles for power between rival élite factions. But at the same time it is clear that at least some of these groups are rooted in movements that existed long before the present crisis. This paper argues that the roots of most of the radical Muslim groups in contemporary Indonesia can be traced to two relatively ‘indigenous’ Muslim political movements which date back to the 1940s – the Darul Islam movement and the Masyumi party – and to a number of more recent transnational Islamic networks. It traces the transformations of Masyumi and Darul Islam from the 1950s and 1960s, the emergence of ‘campus Islam’ in the 1980s, the empowerment of Islam in the final years of the Suharto regime, and the course of Islamic politics during Suharto's downfall and in the 1999 elections, before looking in detail at the recent involvement of radical Muslim groups in street politics.