Background: Excessive apoptosis in the myocardium contributes to the pathogenesis of heart disease. Evidence indicates that high-intensity interval training (HIIT) can alter myocardial apoptosis-related signaling. Objectives: The purpose of the study was to investigate the effect of 12 weeks of HIIT on some indices of apoptosis, including Bcl-2, Bax, and caspase-3 in the myocardial tissue of male rats. Methods: Thirty male Wistar rats (age range: 8-10 weeks) were randomized into three groups, including sham (n = 10), control (n = 10), and HIIT (n = 10). The experimental group underwent HIIT consisting of 2-8 repetitions of 4-min high-intensity intervals (85%-90% peak speed) interspersed with low-intensity intervals (45%-50% peak speed), performed five times/week over 12 weeks. Forty-eight hours after the last training session, animals’ hearts were removed. The gene expressions of Bcl-2, Bax, and caspase-3 were analyzed by the RT-PCR method. The independent t-test was used for statistical analysis (P < 0. 05). Results: The gene expressions of Bcl-2 and Bcl-2/Bax ratio were higher in the training group than in the control group (P = 0. 001 and P = 0. 002, respectively). Regarding Bax and caspase-3 gene expression, although the mean levels were lower in the exercise group than in the control group, the differences were statistically insignificant (P = 0. 57 and P = 0. 27, respectively). Conclusions: Overall, it seems that HIIT significantly increases the expression of anti-apoptotic indicator Bcl-2 and the ratio of Bcl-2/Bax in the myocardium of male rats. However, further studies are needed to show the effects of HIIT on myocardial apoptosis.