Furan has been identified in foods such as heat-treated foods, including coffee, canned meat, hazelnuts, and infant foods and formulas. Children may be exposed to furan via either consumption of these foods or their derivatives. We evaluated the effects of furan on the thymus of weaning male rats in the present study. Five separate groups containing male rats were used: control, oil control, and three furan-treated groups. Furan was given orally to rats in the treatment groups at doses of 2, 4, and 8 mg/kg/day for 90 days. At the end of the experiment, thymus of the rats were examined morphologically, histopathologically, and immunohistochemically. We observed that absolute and relative weights of thymus were decreased significantly in rats treated with 4- and 8-mg/kg/day doses of furan. In histopathological examination, enlargement of interstitial connective tissue between the thymic lobules, lymphocyte depletion, and hemorrhage were observed. We detected an increase in apoptotic cell counts in thymus of the treatment groups. In addition, we found significant differences in the distribution of fibronectin and transforming growth factor-beta in the thymus of the treatment groups. In conclusion, we suggest that furan has affected the thymus in growing male rats.