BACKGROUND Allograft rejection remains a major obstacle to long-term survival in heart transplantation. Recent studies have demonstrated that apoptotic cell death may occur in acute allograft rejection. The purpose of this study was to determine whether apoptotic cell death is involved in rat cardiac allograft rejection through both the perforin/granzyme pathway and the Fas/Fas ligand (Fas-L) pathway. METHODS Groups of Lewis (RT1(1)) rats underwent heterotopic heart transplantation from disparate DA (RT1a) or syngeneic Lewis rats. The cardiac grafts were harvested 1, 3, or 5 days after transplantation and analyzed for apoptotic cell death using DNA nick-end labeling, immunocytochemistry, and electron microscopy. In addition, the expression of granzyme B, perforin, Fas, and Fas-L messenger RNA were analyzed by reverse transcriptase-polymerase chain reaction. RESULTS Apoptotic cell death of cardiac myocytes was prominent in allografts on day 5 after transplantation. Fas gene transcripts were constitutively expressed in both syngeneic and allogeneic grafts, whereas expression of Fas-L was only upregulated in allografts with ongoing rejection. Granzyme B and perforin gene expression were also upregulated in allografts with ongoing rejection. CONCLUSIONS These results suggest that myocyte apoptosis through both the perforin-granzyme pathway and the Fas-Fas-L pathway may be involved in cardiac allograft rejection in rats.