The female reproductive system is highly sensitive to physiological stress. However, the mechanism(s) involved in dysfunction of the ovaries induced by high intensity exercise training remain unknown. In the present study, we established a rat model of high intensity exercise training, and investigated the morphological and functional changes in ovaries. Furthermore, we profiled the differential gene expression in the ovaries between high intensity exercise training rats and control rats by restriction fragment differential display PCR. Differentially expressed genes were validated by real-time PCR. The results showed that the weight and microstructure of the ovaries were significantly altered in the exercise training group rats. In addition, the levels of estradiol, progesterone, luteinizing hormone and follicle-stimulating hormone were significantly decreased in the exercise training group rats compared with the control group rats. Immunohistochemistry revealed weak expression of estradiol, estrogen receptor and progesterone receptor in ovarian tissues from the high intensity exercise training group compared with the control group. Furthermore, the gene expression profiles of the exercise training and control group rats were analyzed, and differentially expressed genes, such as those involved in the ubiquitin-proteasome system, were identified. Our results indicate that high intensity exercise training can suppress the cellular function of the ovary glands. The mechanism may involve a series of alterations in the expression of genes particularly associated with the ubiquitin-proteasome system.