Zinc is an essential element involved in many basic biochemical reactions in thyroid. However, little is known about concentration of this mineral in goitrous Iranian schoolchildren. This study was undertaken to determine the prevalence of zinc deficiency and the current zinc status in goitrous schoolchildren. A cross-sectional study in which 1188 schoolchildren in the age group of 8-13 years were evaluated for goiter prevalence, urinary iodine and zinc status. Zinc measurement was performed by atomic absorption spectrometry apparatus and urinary iodine was measured by digestion method. Goiter was graded according to WHO classification and serum concentration of thyroid hormones and thyroid-stimulating hormone were determined by commercial kits. This study showed an adequate iodine supply. Eleven percent of all cases had low zinc levels and the mean serum zinc concentration was 84.1 +/- 20.7 microg/dl with a significant difference between the boys and girls (86.6 +/- 22.7 microg/dl vs. 82 +/- 18.7 microg/dl, p = 0.017). The mean concentration in goitrous children was 85.1 +/- 23 microg/dl and for those without goiters was 82.6 +/- 16.7 microg/dl which was not statistically significant. No significant difference was noticed between those with low and normal zinc levels in the prevalence of goiter. In view of normal iodine status, other goitrogenic factors should be evaluated to explain the residual goiter prevalence.