In the late 1990s, Indonesians experienced unprecedented levels of ethnic conflict. During 1995 and 1996, riots in Situbondo, Tasikmalaya, and other parts of Java caused numerous deaths and the destruction of private property. They had ethnic and religious overtones that suggested serious tensions cutting across several dimensions of relations between Indonesia's ethnic groups. The wave of riots was perceived, in part, as a new phase in anti-Chinese sentiments that had regularly led to violence against the Chinese before and after Indonesia's independence. The targeting of places of worship, however, had others argue that relations between religious groups were deteriorating and reaching dangerous levels of tension. In either case, the riots were sufficiently different, numerous, and larger in scale from violent events since the 1960s to suggest a worrying trend.

These worries were confirmed in the following years. Between 1997 and 2002, at least 10,000 people were killed in ethnic violence throughout the archipelago. In 1996–97 and 2001, two waves of violent clashes between Dayaks and Madurese in West and Central Kalimantan led to the deaths of at least 1,000 people and the displacement of hundreds of thousands of Madurese. In Maluku, at least 5,000 people were killed in a war between Christians and Muslims that began in January 1999 and escalated during the following three years. In East Timor, approximately 1,000 people were killed and 200,000 displaced in violence against the civilian population, following a referendum in August 1999.