Free transverse rectus abdominis myocutaneous and deep inferior epigastric perforator flaps represent increasingly popular options for breast reconstruction. Although several retrospective, small-scale studies comparing these flaps have been published, most have failed to find a significant difference in flap complication rates or donor-site morbidity. We systematically reviewed the current literature, and subsequently pooled and analyzed data from included studies. Included studies reported flap complications and/or donor site morbidities for both flap types. Eight studies met the inclusionary criteria. For flap complications, there was a statistically significant difference between deep inferior epigastric perforator and free transverse rectus abdominis myocutaneous flaps in fat necrosis rates (25.5 +/- 0.49 vs. 11.3% +/- 0.41%, P < 0.001) and total necrosis rates (4.15 +/- 0.08 vs. 1.59% +/- 0.08%, P = 0.044). Partial necrosis rates were not statistically significant (3.54 +/- 0.07 vs. 1.60% +/- 0.07%, P = 0.057). For donor-site morbidity, there was no statistically significant difference in abdominal bulge (8.07 +/- 0.23 vs. 11.25% +/- 0.29%, P = 0.28). Multicenter, prospective studies are needed to further investigate differences between these flap options.