In this study the effect of propylthiouracil-induced hypothyroidism on rat submandibular salivary gland function and the level of copper and zinc trace elements in serum and saliva were determined. Propylthiouracil (PTU) was administered to rats for 1, 2 and 3 weeks in three different groups to induce hypothyroidism. Pilocarpine was administered under anesthesia and pure samples of saliva were collected to measure flow rate and copper and zinc levels. All the treated groups had a significant reduction in flow rate that correlated to the duration of PTU treatment. The concentration of copper in serum and saliva showed a significant increase, whereas zinc levels did not show a significant change in saliva, and decreased in serum. The weight of the salivary glands in animals treated with PTU for 2 to 3 weeks showed a significant reduction during the medication period. Therefore, we may conclude that hypothyroidism leads to changes in salivary gland function, weight, and also the level of trace elements in serum and saliva.