Poor nutrition and health can affect children’s education. The nutritional status of school children (9-15 years) was assessed in Kumi district, Eastern Uganda in 2006-2007. Selection of schools was done using modified cluster sampling involving 34 schools (n= 645). Assessments for nutritional status were done anthropometrically (height and weight), biochemically (iron, n=145; iodine, n=87; and vitamin A, n=145) and assessment for health status was done following the formal ether concentration technique for examination for intestinal helminths (n=189) and a quick malaria (n=119) test for malaria parasites. Prevalence rates for stunting, underweight and thinness were 8.7% (95CI 6.7-11.1); 13.0% (95CI 10.6-15.8); and 10.1% (95CI 7.9-12.6), respectively of which males and the older age group of children were more affected. Prevalence rates for iodine deficiency, anaemia, iron deficiency and vitamin A deficiency (VAD) were 3.4% (95CI 0.9-9.1); 24.1% (95CI 17.7-31.6); 82.1% (95CI 75.2-87.7); and 30.3% (95CI 23.3- 38.2), respectively. Anaemia (measured as haemoglobin status), iron deficiency (measured as serum Ferritin) and VAD (measured as serum retinol) were higher among females (26.3%, 95CI 17.5-36.7; 83.8%, 95CI 74.4-90.7; 33.8%, 95CI 24.0-44.6) compared to males (21.5%, 95CI 12.8-32.8; 80%, 95CI 69.0-88.4; 26.2%, 95CI 16.6-37.8). Geohelminth (S.mansoni & N.americanus) and malaria parasitemia were 4.8% and 46.2%, respectively. Prevalence rates for stunting, iodine deficiency and geohelminth infections were low. The high prevalence rates of wasting/thinness, underweight, iron and vitamin A deficiencies show these as significant public health problems among school children in Kumi district. There is a need to focus attention on nutritional and health conditions of school children to improve their conditions. Much can be done to prevent malaria infection by promoting the use of Insecticide Treated Nets and chemoprophylaxis. The biennial dosage with albendazole for deworming, and universal use of iodized salt in Uganda are success stories that should continue; iron deficiency anaemia can be controlled through nutrition education, provision of nutritious school meals coupled with control of malaria and deworming. Since many children attend school, such services if delivered through school systems would assist those school children who most need them