There is speculation about madaris in Pakistan as sources of terrorists and about levels and reasons for enrolment, but a dearth of empirical data. We studied madarsah enrolment among 53,960 representative households; 853 focus groups of parents discussed enrolment choices. In 2004, 2.6% of all children (3.8% of school-going children) aged 5–9 years attended a madarsah. Children from urban and less educated households were more likely to attend a madarsah, but there was no difference by sex of the child or household vulnerability. Parents chose madaris because they offered an Islamic education. Our findings challenge misconceptions about madaris in Pakistan.