For several years there is no conclusive guideline on the effectiveness of pulsatile or non-pulsatile perfusion during cardiopulmonary bypass (CPB) in patients undergoing cardiac surgeries. In this study, we evaluated the effect of pulsatile versus continuous perfusion on the myocardial release of the cardiac biochemical markers including, creatine phosphokinase (CPK), cardiac creatine kinase (CK-MB), and lactate dehydrogenase (LDH), and also kidney function tests including: blood urea nitrogen test (BUN) and creatinine test (Cr) in patients that underwent both pulsatile and non-pulsatile methods before and after heart surgeries. A total of 80 patients were enrolled in this study, 40 patients in each pulsatile and non-pulsatile group. Venous blood samples were drown from each patient in two groups before operation and after operation at, 24, 48, and 72 h and analyzed separately for CPK, its cardiac isoenzyme (CK-MB), LDH, BUN and Cr. There were no significant differences between the two groups with regard to preoperative parameters such as sex, age, and body surface area. Our study shows that the effect of pulsatile perfusion on cardiac and kidney function is better than the non-pulsatile method.