Objective: To observe the myocardial protecting effects of Ginaton (Ginkgo biloba extract) on ischemic-reperfusion injured myocardium during cardiopulmonary bypass (CPB). Methods: Twenty patients selected undergoing mitral valvular replacement were randomly divided into two groups. Control group: 10 patients, intermittent intra-aortic infusion with cold St.Thomas solution during hypothermic CPB. Ginaton group: 10 patients, intermittent intra-aortic infusion with cold St. Thomas solution containing Ginaton (0.5 mg*kg-1). Changes of ultrastructure levels of adenosine triphosphate (ATP), malondialdehyde (MDA) and hemodynamic data were measured. Results: Hemodynamic parameters in the Ginaton group were maintained better than those in the control group. MDA in the control group was significantly elevated during ischemic-reperfusion (P<0.05), while in the Ginaton group, there were no obvious change. The levels of ATP and energy change in the Ginaton group were obviously higher than those in the control group at declamping aorta (P<0.05). The percentage of normal mitochondria and glycogen content were significantly higher in the Ginaton group than that in the control group at declamping aorta (P<0.05). Conclusion: Ginkgo biloba extract may provide a beneficial effect on myocardial protection in ultrastructural preservation, prevention of high energy phosphate depletion, reduction in free radicals production and improvement of myocardial function.