This study shows that ischemia and reperfusion induce alterations on the gene expression level in human muscle free flaps. Data from this study indicate that the expression of HIF-1α might not be affected but that other putative pathways of ischemic regulation might be of great interest. Finally, these findings correspond with the surgeon's clinical experience that the accepted times of ischemia, generally up to 90 minutes, are not sufficient to induce pathophysiologic processes, which can ultimately lead to flap loss.