The aim of this study was to ascertain the percentage of apoptotic myocytes in patients who underwent coronary artery bypass surgery. Apoptotic index (AI) obtained with in situ terminal deoxynucleotidyl transferase-labeled dUTP nick end labeling (TUNEL) method and Bak protein expression were compared.Twenty consecutive patients who underwent coronary artery bypass surgery, myocardial samples from the right atrium were taken in three stages: before cannulation (the first sample group), after declamping (the second sample group), and 20 minutes after reperfusion (the third sample group). The percentage of apoptotic cells was determined by TUNEL method. Expression of Bak protein was immunohistochemically analyzed. Intermittent ischemia and moderate hypothermia were used as methods of myocardial management during surgery. A statistical analysis was performed by using the Friedman ANOVA analysis of variances, the Kendall coefficient of concordance and the Wilcoxon matched pair test.In the first sample group mean value of Bak expression was 2.61 +/- 2.18, compared with AI 5.38 +/- 3.58, after declamping (the second sample group) the mean value of Bak expression was 4.31 +/- 2.68 while AI was 7.63 +/- 4.38 and after 20 minutes of reperfusion in the third sample group mean value of Bak expression was 8.89 +/- 4.45, while AI was 15.6 +/- 8.45. When compared by using Wilcoxon matched pair test two methods significantly correlated, p > 0.0001.The positive correlation between AI obtained by TUNEL method and expression of Bak protein may suggest that apoptosis is activated mainly through mitochondrial activation pathway in ischemic reperfusion injury. The results suggest that ischemic reperfusion injury increases the AI in the right atrial tissue. If so, immunohistochemical expression of Bak protein could be used as a marker of myocardial ischemia induced injury.