Although endemic goiter had been recognized in most parts of the country, there are few available data on iodine-deficiency disorders (IDDs) in Mongolia. This study aimed to characterize the current status of iodine deficiency in Ulaan Baatar, Mongolia's capital city. Cross-sectional, observational study designed and performed according to the surveillance methods for IDD prevalence recommended by WHO/UNICEF/ICCIDD. A total of 505 schoolchildren aged 9-14 years (237 girls and 268 boys) and 138 mothers and their neonatal infants were selected to clinical and biochemical examination of the thyroid in 1996 and 1999. The anthropometric measurements, thyroid volume determined by ultrasound, blood TSH and FT4 concentrations, urinary iodine concentration and iodine content of salt consumed in households. Median thyroid volumes based on age were generally higher than those in iodine-sufficient areas and comparative to those reported in mild iodine-deficiency areas. Application of the updated WHO/ICCIDD reference values in iodine-replete European schoolchildren to the Mongolian children aged 10-12 years resulted in a goiter prevalence of 43.3%. The median value of urinary iodine concentration was 152.5 micro g/l (1.20 micro mol/l) and 40.3% of children excreted iodine below 100 micro g/l. Iodized salt (> 40 ppm) was consumed in 63.1% of households and in the children using noniodized salt their urinary iodine concentration was lower than those using ionized salt. In postpartum women, median thyroid volume and urinary iodine concentration were 11.3 ml and 107 micro g/l (0.84 micro mol/l), respectively, and 46% of women excreted less than 100 micro g/l (0.79 micro mol/l) of iodine. Of their neonates, 17.8% had elevated blood TSH levels (> 5 mU/l). In a 1999 survey, the goiter prevalence and ratio of low iodine excretion in schoolchildren decreased to 29.8% and 31.3%, respectively, while median urinary iodine concentration remain unchanged (160 micro g/l; 1.26 micro mol/l). The present study clearly indicates the presence of mild iodine deficiency in Mongolia. Enlarged thyroid gland and normal iodine excretion observed in schoolchildren living in Ulaan Baatar may result from the residual effects of iodine deficiency previously and presumably still exist in the city. Slight reduction in the rate of children with enlarged thyroid and low urinary iodine excretion after the onset of national iodinization programme suggests incomplete normalization of thyroid volume in children and that the correction of iodine deficiency is now in progress in Ulaan Baatar. Further nationwide surveys together with monitoring the progress of the national programme eliminating IDD are required in suburban areas surrounding the city and also in rural areas.