Background and purpose: Exercise plays an important role in the management of multiple sclerosis. The aim of the present study was to compare the effect of resistance and endurance training on the expression of MMP-2, MMP-9 and Timp-1 genes in rats with experimental autoimmune encephalomyelitis (EAE). Method: 24 female C57BL6 mice were divided into four groups: control (Con), sedentary EAE (SED-EAE), EAE with resistance training (RT-EAE) and EAE with endurance training (ET-EAE). After EAE induction, resistance and endurance training was performed for 4 weeks (5 days). Tissue extraction was performed 48 hours after the last training session. 48 hours after the last training session, the tissues were removed. Hippocampal gene expression of MMP-9, MMP-2 and Timp-1 was measured by real-time-PCR. The collected data were analyzed by one-way ANOVA test and Tukey's post hoc test (P<0.05). Results: The main effect of group on MMP-2, MMP-9 and Timp-1 was significant (P<0.05). MMP-2 in CON was lower than SED-EAE and RT-EAE (P<0.05). MMP-9 was higher in SED-EAE and RT-EAE than CON (P<0.05), but there was no significant difference in MMP-2 and MMP-9 between CON and ET-EAE (P>0.05). SED-EAE, RT-EAE and ET-EAE had no significant difference in MMP-9 expression (P>0.05). Timp-1 was higher in CON than SED-EAE, RT-EAE and ET-EAE (P<0.05). However, there was no difference in Timp-1 expression between SED-EAE, RT-EAE and ET-EAE (P>0.05). Conclusion: It seems that exercise training, especially endurance training, can play an effective role in reducing markers related to EAE such as MMP-9 and MMP-2.