Nutritional assessment in the community is essential for accurate planning and implementation of intervention programmes to reduce morbidity and mortality associated with under-nutrition. The study was, therefore, carried out to determine and compare the nutritional status of children attending urban and rural public primary schools in Ife Central Local Government Area (ICLGA) of Nigeria. The schools were stratified into urban and rural, and studied schools were selected by balloting. Information obtained on each pupil was entered into a pre-designed proforma. The weight and height were recorded for each pupil, and converted to nutritional indices (weight for age, weight for height, height for age). A total of 749 pupils (366 and 383 children from the rural and urban communities, respectively) were studied. The overall prevalent rates of underweight, wasting and stunting were 61.2, 16.8 and 27.6%, respectively. In the rural area these were 70.5, 17.8 and 35.8%, while in the urban they were 52.2, 15.9 and 19.8%, respectively. The mean nutritional indices (Weight for Age, Weight for Height and Height for Age) were found to be significantly lower among the rural pupils than urban pupils (P < 0.001 in each case). The present study shows that malnutrition (underweight, wasting and stunting) constituted major health problems among school children in Nigeria. This is particularly so in the rural areas. Therefore, prevention of malnutrition should be given a high priority in the implementation of the ongoing primary health care programmes with particular attention paid to the rural population.