We have previously reported the elimination of iodine deficiency and increasing prevalence of autoimmune thyroiditis (AIT) among schoolchildren in northwestern Greece. This study followed up 29 children (12-18 years old) with AIT for 5 years to track its course in the postiodination era. At diagnosis, thyroid peroxidase autoantibodies (TPOAbs) were positive in 25 children (86%) and became positive in all children during follow-up. Thyroglobulin autoantibodies (TgAbs) were positive in 17 children at diagnosis (59%) and became positive in 3 more children (69%). Both antibody types increased by the end of the observation period (p < 0.005). Regarding thyroid function, 7 children (24%) at diagnosis had subclinical hypothyroidism that persisted and 4 more children developed subclinical hypothyroidism during the study period (38%). Only 5 of these children (45%) had positive TgAbs. There was an increase in thyrotropin (TSH) so that at the end of the study all children had TSH greater than 2.5 mU/L but none developed overt hypothyroidism. Thyroid hypoechogenicity that increased over time was seen in all children, especially in those with subclinical hypothyroidism. In conclusion, both antibody types increased in frequency and level, but TPOAbs were the predominant autoimmunity marker predictive of impending thyroid failure in children with AIT, as was thyroid hypoechogenicity on ultrasound.