Selenium deficiency can have adverse effect on thyroid metabolism and response to iodine supplementation. The aim of this study was to determine relationship between prevalence of goiter, thyroid hormone profile, urinary iodine and serum selenium concentrations in Iranian schoolchildren. In a cross- sectional study, 1188 schoolchildren in the age group of 8-13 years were evaluated for goiter prevalence. Urine and serum samples were collected from 500 children and assayed for urinary iodine concentration, thyroid hormone profile and serum selenium concentration. The overall goiter prevalence was 39.6% and the median urinary iodine excretion, indicated to an adequate iodine intake. The mean serum selenium concentration was 119.1 +/- 31 mug/l with significant difference between boys and girls (108.4 +/- 26.2 mug/l vs 127.7 +/- 32.1 mug/l). An increase in free T4 concentration was observed in those with a lower selenium level and there was a significant relationship between the presence or absence of goiter and serum selenium concentration. Selenium supplementation may be an advisable measure to optimize thyroid hormone metabolism and decrease the prevalence of goiter in schoolchildren with low serum selenium concentration.