Beginning in the mid-1990s, there was a sudden rise in violent ethnic conflict in Indonesia. Two aspects that require explanation are the timing and clustering of this type of conflict historically. Other studies have not adequately explained these aspects. Methodological and thematic choices have generated problems with identifying and explaining clustering. Microlevel studies fail to account for the broader changes occurring at a macrolevel. Some researchers have chosen to broaden the scope of analysis of violent events to provide explanations of violence more generally. After reviewing these other studies, I argue that a historical institutionalist approach remains best able to explain the clustering of conflicts and the following period of stability. Changing institutional contexts at critical junctures created rising anxieties as well as opportunities to renegotiate group inclusion and status in the Indonesian state.