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Reverse cholesterol transport (RCT) is a process that prevents atherosclerosis. Studies showed that exercise training for strengthening cardiac muscle, increasing heart lipid metabolism and its potency against risk factors could protect cardiovascular health. Thus, the present study aims to investigate the effects of high intensity interval training (HIIT) on RCT and its related elements in plasma and tissues (liver and intestine) of rats.Twenty adult male Wistar rats were randomly divided into control (n = 10) and trained (n = 10) groups. The trained group undertook HIIT (90%–95% of VO2max, five days/week, for 10 weeks) on a treadmill. The rats were killed five days after the last training session to minimize the effects of the last training session.A higher and significant ABCA1 mRNA was observed in the liver and intestine of trained rats. However, ABCG1 and LXR expressions only increased in the liver following the HIIT. These changes in the expression of the trained rats were accompanied by higher changes in plasma LCAT and HDL levels.The responses of ABCA1, as a key player in plasma HDL biogenesis, are similar in liver and intestine tissues after the HIIT program. However, different responses of ABCG1 and LXR in the liver and intestine tissues of the trained rats confirm the main role of the liver than the intestine in HDL biogenes. Therefore, HIIT modality result in cardiovascular protection by increasing the expression of genes involved in RCT and biogenesis of HDL.