The secular and nationalist emphasis in public schools has been resisted by some of the Muslim majority. A distinct and vocal minority of these Muslims prefer to place their children in a pesantren (Islamic boarding school), or Islamic school. Usually located in rural areas and directed by a Muslim scholar, pesantren are attended by young people seeking a detailed understanding of the Quran, the Arabic language, the sharia, and Muslim traditions and history, as well as more modern subjects such as English, mathematics, and geography. Students can enter and leave the pesantren any time of the year, and the studies are not organised as a progression of courses leading to graduation. Although the chief aim of pesantren is to produce good Muslims, they do not share a single stance toward Islam or a position on secularism. Some pesantren emphasise the autonomy of modern students to think for themselves and to interpret scripture and modern knowledge in a way that is consistent with the teachings of Islam.
Others are more traditional and stress the importance of following the wisdom of elders, including their teachings on science, religion, and family life. Although the terrorist bombings in Kuta, Bali, in 2002 raised suspicions about whether pesantren promote extremist views, the majority of these schools in Indonesia are theologically moderate, reflecting the views of the Indonesian population as a whole. For those who opt for a pesantren education, a sixth-grade equivalency certificate is available after successful completion of a state test.
In order for students to adapt to life in the modern nation-state, in the 1970s the Muslim-dominated Department of Religion (now the Department of Religious Affairs) advocated the spread of a newer variety of Muslim school, the madrassa. This kind of school integrates religious subjects from the pesantren with secular subjects from the Western-style public-education system. Although in general the public believes that Islamic schools offer lower-quality education, among Islamic schools a madrassa is ranked lower than a pesantren.
Madrasah Ibtidaiyah (MI) is the Islamic schooling alternative to SD, following a curriculum with more focus on Arabic and Islam. Madrasah Tsanawiyah (MTs) is the Islamic schooling equivalent of SMP. Madrasah Aliyah (MA) is the Islamic schooling equivalent of SMA while Madrasah Aliyah Kejuruan (MAK) is the equivalent of SMK.