In the 1960s and 1970s, Islamic education in Southeast Asia was not a topic of great scholarly or policy urgency. Although a few anthropologists recognized that Islamic boarding schools in Java, Malaysia, and southern Thailand played an important role in religious learning and the sustenance of local religious identities, the general assumption was that Islamic schooling was so incapable of keeping up with the demands of the modern age that it was just a matter of time before it was pushed from the national scene. In an otherwise thoughtful essay, one of today's most perceptive observers of Islamic affairs in Southeast Asia reached just such a pessimistic conclusion about the future of the Javanese variant of the Islamic boarding school known as the pesantren, writing, “The pesantren has enjoyed an unusually long life for a traditional school, but it may finally be threatened with disappearance.”

As it turns out, like its southern Thai counterpart, the Javanese pesantren did not disappear. Rather, like Islamic education across most of Muslim Southeast Asia, it has flourished and diversified since the great resurgence in Islamic piety of the 1970s and 1980s. At the same time, however, Muslim educational institutions are no longer seen as quaintly irrelevant institutions. Since the 9/11 attacks in the U.S. and the October 2002 Bali bombings in Indonesia in particular, the sense of wistful obsolescence that used to characterize discussions of Southeast Asia's Islamic schools has been replaced by an anxious and often unhelpful media frenzy.

The reasons for the change of perception are understandable enough. The teachers of the young men responsible for the October 2002 attack in Bali had educational ties to the al-Mukmin boarding school in Central Java, an institution alleged to have links to the terrorist Jemaah Islamiyah. The link led to widespread fears that some of Indonesia's 47,000 Islamic schools were being used to open a “second front” in the al-Qa`ida conflict with the West. In the Philippines, the Intelligence Chief of the Philippine Armed Forces blamed an upsurge in terror bombings in that country in the early 2000s on the southern Philippines’ network of madrasas.: “[T]hey are teaching the children, while still young, to wage a jihad. They will become the future suicide bombers.”