Abnormal regulation of apoptosis is observed in ischemic injury and may contribute to the pathogenesis of atherosclerosis. However, its role in cardiac allograft vasculopathy (CAV), the fundamental lesion of the chronic rejection (CR) in heart transplantation, remains uncertain. To clarify this issue, apoptosis in myocardium and coronary arteries from five cardiac allograft donors (NL) and explanted hearts of 24 patients with ischemic cardiomyopathy (IsCM) and 15 patients with CR was quantitated by end-labeling of fragmented DNA (TUNEL) and immunoblotting for activated caspase 3 and caspase 9. Myocyte apoptosis assessed by TUNEL was similarly increased over NL (0.21%) in both CR (0.88%, p<0.01) and IsCM (0.88%, p<0.01). Activated Caspase 9 was significantly higher in CR (14.7%) compared to that in IsCM (6.9%, p<0.01) and NL (0%), while activated Caspase 3 was similarly elevated in both CR and IsCM (7.8% and 6.5% vs 0% in NL, p<0.01 and p<0.05). Myocardial Bcl-2 and Bax expression was increased in CR compared to both NL (Bax: 4.3-fold, p<0.01; Bcl-2: 5.9-fold, p<0.01) and IsCM (IsCM: Bax: 2.2-fold, p<0.05, Bcl-2: 3.2-fold, p<0.01). The rate of apoptosis and Bcl-2:Bax ratio independently correlated to graft survival in CR (Activation of Caspase 9: r=0.87, p<0.01; Bcl-2:Bax: r=0.57, p=0.05). Coronary arteries with CAV showed more medial apoptosis (7.8-fold, p<0.01) and higher Bcl-2 (5.1-fold, p<0.01) with lower Bax (3-fold, p<0.05) in the intima compared to native atherosclerosis. These results indicate that abnormal Bcl-2 and Bax expression in myocardium and coronary arteries of cardiac allografts with CR is distinct from that in IsCM, and suggest balancing of Bcl-2 to Bax in transplanted hearts promotes long-term graft survival.