BACKGROUND This study was carried out in Lagos State in Ikorodu LGA (rural), a largely agrarian area producing raw materials for agro-allied industries and Ikeja LGA (urban), a highly-developed metropolis and commercial centre. Hitherto, studies showed that undernutrition had been the main form of malnutrition among Nigerian children. However with influences from urbanization, westernization and globalization in cosmopolitan Lagos, it is imperative to find out if the global epidemic of overweight and obesity has caught on. OBJECTIVE To compare the nutritional status of primary school pupils in urban and rural LGAs in Lagos State, Nigeria. METHODS This was a cross , sectional comparative study. A multistage sampling method was adopted. Data were collected from 529 pupils with an interviewer administered questionnaire. Their weight and height were recorded in pre-designed proforma and converted to nutritional indices. RESULTS The prevalence rates of underweight, stunting and wasting in the rural area were 49.6%, 50.8% and 24.2% respectively; while it was 15.1%, 16.6% and 13.6% in the urban area respectively. There was overnutrition in the urban area: 15.1% were overweight and 13.2% were obese. The mean nutritional indices were significantly lower among the rural pupils than urban pupils (p<0.001) in each case. CONCLUSIONS Undernutrition is still a major health problem among school children in Lagos State, Nigeria, more so in the rural area. There is an emergence of overweight and obesity in the urban area. A comprehensive programme to improve nutritional status is recommended as part of a well funded school health programme.