Early detection of a compromised circulation of free flaps and an immediate revision may lead to higher rates of flap salvage. The aim of this study was to evaluate the perfusion of the entire flap using dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI). DCE was performed in 11 patients after flap transplantation using an optimized 3D gradient echo sequence to cover the whole flap. The percentage increase of signal intensity over time was evaluated for the free flap as well as for a reference tissue. Furthermore, normalized signal increase was calculated as the ratio of signal increase within the flaps to the signal increase in the reference tissue. Signal increase in free flaps and reference tissue was compared using the Wilcoxon-test (p < 0.05), normalized signal increase in normally perfused (n = 9) and in flaps with compromised perfusion (n = 2) using Mann-Whitney-test (p < 0.05). Signal increase within normally perfused flaps was similar to the reference tissue. In flaps with compromised perfusion the increase was significantly lower than in reference tissue. Normalized signal increase in adequately perfused flaps and flaps with compromised perfusion also showed a significant difference. DCE MRI may be a valuable non-invasive tool to evaluate tissue perfusion of the complete free flap.