Cardioplegic arrest is one of the most common myocardial protection strategies. A wide variety of cardioplegic solutions are routinely being used. There is an ongoing discussion about the relative effectiveness of these solutions considering myocardial protection. This study aims to investigate the hypothesis that the use of histidine-tryptophan-ketoglutarate (HTK) cardioplegia leads to decreased ischemic damage on myocardium compared with the use of conventional crystalloid cardioplegia. The study population was 32 patients operated on at Başkent University, Department of Cardiovascular Surgery for congenital heart diseases. The first group of 16 patients received conventional crystalloid cardioplegia (KK group) which is a modification of St. Thomas' solution, while the second group of 16 patients received HTK solution (HTK group). The echocardiographic measurements and the laboratory values of the patients were taken as the clinical variables. Right ventricular biopsies were taken from every patient before and after cardioplegic arrest. These biopsies were histopathologically examined for apoptosis using caspase-3 antigen and cell proliferation using Ki-67 antigen. The statistical analysis revealed no significant difference between the two groups regarding the clinical variables, apoptotic indices and proliferation indices. The apoptotic indices in the postcardioplegic arrest biopsies positively correlated with aortic clamp time in the KK group but not in the HTK group. Liver function tests on postoperative day 1 positively correlated with aortic clamp time in both groups. On postoperative day 2, this correlation was sustained in the KK group and ceased in HTK group. The difference in the correlation of apoptotic indices and liver function tests between the groups is accepted as a supportive finding for HTK solution. However, it can be postulated that when the aortic clamp times are similar to those in the present study, the clinical manifestation of the difference between the two solutions would not be significant.