Thymoquinone (TQ) is a phytochemical compound found in the plant Nigella sativa. It has antioxidant and anti-cancer effects. This study investigated the effects of TQ on obesity and testicular structure of high-fat-diet (HFD) fed rats. Obese control (OC) and obese thymoquinone (OT) groups were fed a special diet containing 40% of total calories from fat. Non-obese control (NC) and non-thymoquinone (NT) groups were fed a standard diet for nine weeks. Then, intraperitoneal TQ injections were carried out to the OT and NT groups for six weeks and testes were removed. Catalase and myeloperoxidase activity were determined in rat testis tissue. Stereo logical, histopathological, and immunohistochemical changes were evaluated in the testes of the rats. In stereological studies, mean volumes of testis and seminiferous tubules, the number of spermatogenic cells and also Leydig cells in the OC group were reduced, but these values significantly increased in the OT group. Apoptotic cells were observed in the OC group in comparison to the OT group. The number of healthy sperms were reduced in the OC group, whereas the majority showed anomalies in the head, neck, and tail. The number of healthy sperm was increased and the anomalies significantly reduced by using TQ in both the NT, and especially the OT group. TQ like antioxidants may improve fertility by means of increasing the healthy sperm number and preventing sperm anomalies.