This study compares age at enrolment in Primary School with a range of nutritional measures for 8-9 year old and 12-13 year old children in Ghana (n = 1566) and Tanzania (n = 1390). The results show that short stature (height-for-age z-score), but not other nutritional variables (weight-for-age and weight-for-height z-scores and haemoglobin concentration), is strongly associated with late enrolment. This relationship holds for both age group, sexes and countries, and is independent of socio-economic status in Tanzania (where this parameter was assessed). The relationship between stature and age-appropriate grade becomes less marked with progression through school, which is compatible with a higher drop out rate for more stunted children. These results suggest an important role for health in education; that stunted children enrol later in school and are more likely to drop out earlier.