Background: Effects of soy-containing infant formulas on the thyroid gland is not clear We aimed to evaluate the effects of infant formulas with different quantities of soy content on the functional and histopathological characteristics of the thyroid gland. Method: Twenty-eight female Sprague-Dawley rats were divided into four groups. Group 1 was fed with standard pellet rat food (8g/day); Group 2 soy-free infant formula (8g/day); Group 3 low-dose (1.12g/100ml) soy-containing formula (8g/day), and Group 4 high-dose (2.64g/100ml) soy-containing formula (8g/day). Blood samples were collected from the subjects on day 0, 30, 60, and 90 to evaluate thyroid functions. All subjects were sacrificed on day 90. Thyroid glands were excised and examined histopathologically. Results: Serum levels of free T3, free T4, TSH, anti TPO, and anti TG were significantly higher in Group 4 compared to other groups (p<0.001, p<0.01,p<0.001,p=0.002). No differences were found in the histopathological findings between the groups. Conclusion: Infant formulas with high soy content induce hyperthyroidism with high TSH levels. High levels of anti TPO and anti TG suggest that observed changes might have occurred via inflammatory mechanism.