Background: Reverse cholesterol transport (RCT) is a crucial procedure for preventing Atherosclerosis, and ATP-binding cassette 1 (ABCA1) is a key factor in it. Objectives: The purpose of this study was to examine the effects of two months of a cardiac rehabilitation program on ABCA1 gene expression and other indices of RCT in Coronary artery bypass grafting (CABG) patients. Methods: In this quasi-experimental study, 24 CABG patients were assigned to the cardiac rehabilitation (n = 12) and control (n = 12) groups. The CR group performed two months of cardiac rehabilitation program while the CON group was asked to stay sedentary at home. 48 hours before and after starting the program, 10 cc of blood was sampled for q-RT PCR and biochemical analysis. Results: ABCA1 expression and plasma HDL-C concentration elevated in the CR group following two months of rehabilitation program compared to the CON group (F = 23.66, P = 0.0002 and F = 5.52, P = 0.034, respectively). In addition, in the CR group, there was no significant change in plasma LDL-C and triglyceride (F = 1.89, P = 0.191 and F = 1.61, P = 0.213, respectively). Conclusions: Based on our findings, it can be concluded that two months of CR program elevate lymphocyte ABCA1 mRNA expression coinciding with increased levels of plasma HDL-C. The present results also indicated that the CR program must be seriously considered for CABG patients to improve reverse cholesterol transport and hence, attain the cardiovascular benefits.