Described as “terrorist factories”, the South Asian madrasas have become the subject of great controversy since September 11, 2001. In Afghanistan, people commonly blame Pakistani madrasas for recruiting Afghan youth into militant groups. In response, the Afghan government has initiated a comprehensive reform of the Islamic education sector. Yet, little analytical attention has been paid to Afghan madrasas and their transnational links. This article examines more closely the role of religious education in Afghanistan, transnational connections with madrasas in Pakistan, the alleged links to militancy, and the scope for reform of the religious education sector in Afghanistan.