In order to determine the prevalence of micronutrient deficiencies (iron, zinc and folate) in Sri Lankan adolescent school children and the extent to which multiple micronutrient deficiencies exist in this population, a cross-sectional survey (2003) in the Galle district of the micronutrient and anthropometric status of 945 school children of ages 12-16 years was performed. The prevalence of anemia (Hb < 120.0 g/L) was 49.5% in males and 58.1% in females (overall 54.8%, gender difference, P = 0.004). In anemic children 30.2% of males and 47.8% of females were iron deficient (serum ferritin < 30.0 microg/L). Folate deficiency (<6.80 nmol/L) was found in 54.6% and 52.5% of boys and girls respectively whereas zinc deficiency (<9.95 micromol/L) occurred in 51.5% and 58.3%. Anemic boys had a 1.5 (95% confidence interval (CI) 0.9-2.6) and 1.6-fold (CI; 1.1-2.6) greater risk of being stunted and underweight, whereas the risk among anemic girls was 1.7 (CI; 1.1-2.7) and 1.0 (CI; 0.7-1.5) for being stunted and underweight. The relative risks of having at least two deficiencies in iron, zinc and folate among anemic children were 1.6 (CI; 0.6-4.2) among boys and 0.8 (CI; 0.5-1.5) among girls. Iron deficient subjects had a significantly increased risk of 1.8 (CI, 1.1-3.0) of being deficient in folate and 1.7 (CI, 1.2-2.6) of being deficient in zinc. Zinc deficient subjects had a risk of 1.3 (CI, 1.0-1.8) being iron deficient and 1.2 (CI, 0.9-1.7) of being folate deficient. Multiple micronutrient deficiencies are prevalent in Sri Lankan adolescents.