Objective The reasons for the difference in life expectancy between males and females are still unknown. Previous studies have provided compelling evidence for the presence of oxidized proteins, and lipids in advanced human atherosclerotic lesions. The gender factor responsible for such protein oxidation is unknown and controversial. Our aim was to reveal the difference between myocardial protein and lipid oxidation parameters of male and female aged rats. Methods We investigated the relation between myocardial protein carbonyl (PCO) and other protein oxidation parameters such as advanced oxidation protein products (AOPP), nitrotyrosine (NT), protein hydroperoxide (P-OOH), and protein thiol (P-SH). Our study also covered other oxidative stress parameters, such as total thiol (T-SH), non-protein thiol (Np-SH), 4-hydroxyalkenal (4-HAE), malondialdehyde (MDA), reduced glutathione (GSH), and the glutathione disulfide (GSSG). Results Among the studied parameters, myocardial PCO, AOPP, NT, Np-SH, GSH, Fe2+ levels and the redox index (RI) of male rats were significantly higher than in the female group. On the other hand, P-OOH, P-SH, T-SH, 4-HAE, and MDA levels were all found to be not different. Conclusions These data support the hypothesis that elevated levels of PCO, AOPP, and NT contribute to the extent of protein, but not lipid, oxidation in aged male rats. We are of the conviction that the increased myocardial Np-SH, GSH and RI levels that we have determined in aged male rats may be a protective factor in propagation of protein oxidation. Our findings support our conviction that protein and lipid oxidation, in the myocardial tissue of aged rats, have a controlling role in differing regulating mechanisms through gender differences.