Madrassahs, which are Islamic boarding schools that provide general education and education in the principles of Islam, are believed by some to be an important vehicle for the recruitment/networking of fundamentalist Islamic terrorists. Others, however, argue that only a small percentage of madrassahs promote radical Islamic beliefs that become the motivation for joining terrorist groups. This article addresses this debate from data derived from Indonesia and Malaysia, acknowledging that the proposed argument cannot be generalized to South Asia (Pakistan) or all of Southeast Asia, where madrassahs are also important. This article uses the case of Jemaah Islamiya (JI), the Islamic terrorist organization in Indonesia and Malaysia, to present its argument. First, the JI-linked radical madrassah attendance rates by those involved in terrorist operations are significantly higher than that of the Indonesian population as a whole, suggesting that madrassahs have may have an association with terrorism. Second, the analysis shows that only JI-linked radical madrassah attendance, not all madrassah attendance, is linked to an increased role in the Bali, Marriott, and Australian embassy bombings; therefore, analysts should be careful in making broad proclamations about the links between madrassahs and terrorism. This caution is particularly warranted in Indonesia, where there are approximately 14,000 madrassahs, many of which are state-regulated and managed. Third, the analysis shows that JI-linked radical madrassahs act as focal points that assist in bringing together like-minded radicals, who can be easily guided into terrorist training and attacks. Thus, radical madrassahs can influence both the belief system and the skill set necessary to be a terrorist. 4 tables, 58 notes, 2 case studies, and appended tabular statistics for independent variables