Background: The purpose of this study was to investigate whether and how the extracorporal perfusion of muscle flaps with a miniaturized perfusion system could change the expression of the proapoptotic protein caspase 3 and of the ischemia-sensitive protein hypoxia-inducible factor (HIF)-1α as a first step toward the development of a clinically reliable tool for circumventing ischemia problems in free muscle flap transfer. Methods: In this study, 25 porcine rectus abdominis muscles were used and assigned to five different groups. In the baseline group (group I), the muscle flap remained in situ; in groups II and III, the muscle flap was harvested and remained ex vivo without or with subsequent single-shot heparinized flush; and in groups IV and V, the flaps were perfused with either heparinized autologous whole blood or crystalloid fluid (Jonosteril), using a miniaturized perfusion system without Exogen oxygenation. Muscle samples were taken for immunohistochemical evaluation. The proportion of positive cells for HIF-1α and caspase 3 was compared for each group (groups II through V) to the baseline group (group I). Results: The expression of HIF-1α and caspase 3 was increased in both groups without perfusion and was low during in vivo perfusion and extracorporal perfusion with crystalloid fluid. Heparinized autologous whole blood perfusion shows no protective effect, in contrast to the crystalloid fluid. Conclusions: The data of this study indicate that the extracorporal perfusion of muscle flaps with crystalloid fluid is a possible protective strategy against ischemia. Autologous heparinized whole blood seems to have no additional protective effect in a pure perfusion setting without oxygenation.