Northwestern Greece was identified in the 1960s for its high prevalence of endemic goiter and iodine deficiency. Although iodized salt has been commercially available since then, a recent epidemiological survey of 3916 schoolchildren found that low-grade goiter is still prevalent in endemic proportions (21%). The aim of this study was to further assess the cause of goiter and the severity of iodine deficiency in children from this endemic area of Greece. Of the 800 children with clinically detectable goiter, 97 children (60 girls and 37 boys, 8-15 years) were recruited for determination of urinary iodine excretion, as well as assessment of thyroid volume and function and detection of antithyroid antibodies. The median urinary iodine concentration was 8.4 microg/dL, indicative of a mild iodine deficiency. Thyroid function was normal in all but 11 children who had subclinical hypothyroidism. Sixteen children (16.5%), including all those with subclinical hypothyroidism, were positive for antithyroid antibodies. Their median urinary iodine concentration (20.6 microg/dL) was higher compared to children who were negative for antibodies (7.4 microg/dL; p<0.001). The mean thyroid volume by ultrasonography (12.2+/-4.1 mL) was above the upper limit of normal for this age group. Thyroid volume was inversely related to the urinary iodine content in the children with negative antithyroid antibodies. Iodine deficiency is still prevalent in northwestern Greece although of mild severity and constitutes the primary cause of goiter among schoolchildren. However, it appears that autoimmune thyroiditis is emerging as a frequent cause of goiter in those children with sufficient iodine intake.