Background: Recently, new risk factors for cardiovascular disease are known that include homocysteine levels and C-reactive protein. Due to lack of consensus on the role of exercise on plasma homocysteine levels, in this study, the effect of one session endurance swimming training on plasma levels of homocysteine and atherogenic index of rats were measured. Materials and methods: Totally, 14 male Wistar rats with weight range of 180 ± 20 g were randomly and matched by weight assigned to experimental (n=7) and control (n=7) groups. Experimental group participated in endurance swimming training protocol for 60 minutes. During the first two weeks familiarity of animals with the practice sessions was done in a way that during these meetings, duration and intensity exercise increased gradually until the rats could swim with overload (5% of their weight) for 60 minutes. Blood samples were collected 24 hours after the main activity of protocol from unconscious mice directly from the heart and with the maximum possible amount. Independent t-test and paired t-test were used for data analysis. Results: The results of the study showed that there was a significant difference in homocysteine levels between two groups (p<0.05). However, there was no difference in HDL and total cholesterol between two groups. Conclusion: The findings of present study showed that one session of long-term endurance swimming with low intensity can significantly impact on reducing homocysteine levels which can result in decreasing the risk of cardiovascular disease.