A cluster survey of the age, sex and enrolment status of all school-age children 5-14 years old was undertaken in 2006 in a remote rural sub-district of the Northwest Frontier Province, Pakistan about a year after a devastating earthquake. Information was collected on the characteristics of children, their households and parents, and on reasons for non-enrolment. The health and nutritional status of a randomly selected child in each household was assessed and enrolled and non-enrolled children were compared by sex. A total of 2032 children were recorded in 925 households, 845 girls and 1187 boys, a sex ratio of 71 girls/100 boys. Half of all girls were not enrolled in school compared with a fifth of all boys. There was no common reason for non-enrolment and they differed between the sexes. The randomly selected children (n = 897) were moderately malnourished: 43% were stunted, 12% were thin and 46% were anaemic. 66% of a sub-sample of children (n = 269) had a low urinary iodine concentration, which could contribute to a low IQ and impaired hearing. There were no statistically significant differences in the nutritional status or health of non-enrolled and enrolled girls. These data contribute towards an understanding of how to improve the education and health of school-age children in a conservative, rural province of Pakistan.