BACKGROUND The choice of microsurgical anastomotic technique, end-to-end (ETE) or end-to-side (ETS), is a relevant point in free tissue transfer. The decision-making process of choosing ETE or ETS technique depends on several clinical and perioperative factors. This study evaluates the outcomes of microvascular procedures in a large single centre patient series, focusing on ETE vs ETS arterial anastomoses. METHODS Between January 2009 and June 2015, 838 patients underwent free flap surgery for reconstruction after trauma, infection, or malignancies. The cases were divided according to the microsurgical technique of the arterial anastomosis into an ETE (n = 693) and an ETS (n = 145) group. The series was retrospectively analysed and the two groups compared regarding outcomes. RESULTS Overall, there was no significant difference in rates of surgical complications, flap failures, and re-explorations between the patient groups during the 3-months follow-up period. CONCLUSIONS The presented analysis includes a large series of microsurgical reconstructions evaluating outcomes in respect to type of performed arterial anastomosis. While the decision of performing an ETE or ETS arterial anastomosis must be made according to recipient vessel quality and accessibility, given no change in outcomes, an ETS anastomosis should be performed whenever feasible in order to preserve distal perfusion.