BACKGROUND Iodine deficiency is a major health problem worldwide. Goiter prevalence and the median urinary iodine concentration in a population usually define endemic iodine deficiency. In addition to goiter prevalence and median urinary concentration, thyroid stimulating hormone (TSH) and thyroxine have been used as iodine deficiency indicators. OBJECTIVE To evaluate endemic goiter prevalence in Western Anatolia, Turkey, and to evaluate the sensitivity of thyroglobulin and height percentile as iodine deficiency indicators. SUBJECTS We examined 727 school-children (378 girls, 349 boys) in two cities (Bolu and Düzce) and six mountainous rural areas, in West Anatolia. Of the 727 children, 234 were from four urban schools, and 493 were from eight rural schools. METHODS Clinical examination and ultrasonography were used to evaluate goiter prevalence. Iodine in spot urine, serum total thyroxine (T4), serum free thyroxine (FT4), thyroid stimulating hormone (TSH), and thyroglobulin (Tg) were measured. Iodine deficiency severity was classified based on thyroid volume measurements by ultrasonography and urinary iodine excretion. RESULTS The degree of iodine deficiency according to concentration of urinary iodine was severe in 276 children (38%), moderate in 151 (20.8%), mild in 114 (15.7%), and within normal levels in 186 (25.4%). Although urban areas showed normal or mild urinary iodine excretion, four rural areas showed from mild to severe iodine deficiency (p < 0.001). Thyroid volumes of the severe iodine deficiency group were significantly higher than those of moderate and mild iodine deficiency groups (p < 0.001). There was no significant difference between thyroid volumes in moderate and mild iodine deficiency groups. FT4 levels of the severe iodine deficiency group were significantly lower than in moderate and mild iodine deficiency groups (p < 0.001). There was no significant correlation between TSH and iodine excretion (r = 0.01, p > 0.05). Thyroglobulin (Tg) levels were significantly different between all groups (p < 0.001). There was a significant negative correlation between Tg and urinary iodine excretion (r = -0.27, p < 0.001). CONCLUSIONS Severe and moderate iodine deficiency areas are more prevalent in Turkey than mild and normal iodine concentration areas. In addition to urinary iodine concentration and thyroid volume, height percentile and Tg are also sensitive markers for endemic iodine deficiency. TSH screening should be performed nationwide in Turkey. We recommend compulsory iodination of table and industrial salt.