An attitude scale measuring tolerance has been used with a sample of 350 students in Pakistani religious schools (madrasas). Sectarian affiliation was identified as a key variable, which was moderated by student gender. Female students in general scored negatively, especially if they identified as Deobandi. Shiʿi and Barelvi students are more likely than not to show positive tolerance of others. Cluster analysis separates the students into ‘conservatives’ and ‘liberals’. Shiʿa show a strong liberal tendency, while Deobandis show a strong conservative tendency. Results are consistent with the emergent theology of the groups and the aggressive elements in Pakistani society. Suggestions are made for the mechanism of curricular change in the liberal Shiʿi and Barelvi madrasas and for the direction of research into the Deobandi and Ahl-i Hadith schools.