Islam is Indonesia's dominant religion with approximately 88% of its population identifying as Muslims, making it the most populous Muslim-majority nation in the world.

The Indonesian Central Statistic Bureau (BPS) conducts a census every 10 years. The latest data available, from 2000, drew on 201,241,999 survey responses; the BPS estimated that the census missed 4.6 million persons. The BPS report indicated that 88.22 percent (210 million in 2004) of the population label themselves Muslim, 5.87 percent Protestant, 3.05 percent Catholic, 1.81 percent Hindu, 0.84 percent Buddhist, and 0.2 percent "other," including traditional indigenous religions, other Christian groups, and Judaism. The country's religious composition remains a politically charged issue, and some Christians, Hindus, and members of other minority faiths argue that the census undercounted non-Muslims.

Most Muslims are Sunni, although some follow other branches of Islam, including the Shia, who number approximately 100,000 nationwide. In general the mainstream Muslim community belongs to two orientations: "modernists," who closely adhere to scriptural orthodox theology while embracing modern learning and modern concepts; and predominantly Javanese "traditionalists," who are often followers of charismatic religious scholars and organized around Islamic boarding schools.