The present study conducted proteomic analysis to identify ovarian proteins induced by GnRH/GnIH in comparison with untreated control mice. We used methods of 2-dimentional gel electrophoresis and LC-MS/MS for protein identification. Out of the 25 differentially expressed spots from each of the GnRH/GnIH treated ovaries we were randomly selected 18 protein spots identified by LC-MS/MS. The proteins 14-3-3, prohibitin and superoxide dismutase (SOD1) identified by LC-MS/MS were further verified by Western blotting, which confirmed that GnRH/GnIH-induced changes in expression of 14-3-3, prohibitin and SOD1 were similar to the observations of proteomics. These selected proteins, 14-3-3, prohibitin and SOD1, were further have been the correlation with various ovarian activities, such as cell proliferation, survival or markers of apoptotic. Out of 18 identified GnRH-induced proteins, 9 showed up-regulations whereas other 9 showed down-regulations. This finding suggests that GnRH acts both by stimulating and inhibiting expression of protein. Interestingly, in the GnIH-induced ovary, 15 out of 18 proteins were significantly down-regulated suggesting that, GnIH acts mainly by inhibiting the expression of proteins involved in ongoing ovarian activities. Thus, the present study indicates many of the identified GnRH/GnIH-induced proteins are potentially linked to ovarian follicular development, atresia, steroidogenesis and cancer.