Objective To study apoptosis after vascularized compound tissues transplantation (VCTT) and to evaluate the role of apoptosis in ischemia-reperfusion injury (IR injury). Methods Apoptosis after VCTT was analyzed by flow cytometry (FCM), transmission electron microscopy (TEM), TdT-mediated dUTP nick end labeling (TUNEL) assay, and DNA ladder gel electrophoresis. Results At 6 h after ischemia-reperfusion, typical apoptotic cells were observed by TEM in graft tissues. Six, 12 h after ischemia-reperfusion, positive cells were checked by TUNEL assay and apoptosis rate was 20% by FCM analysis in IR groups. Conclusion There was apoptosis in VCTT and apoptosis might play an important role during IR injury.