This study aims to compare the use of Bemiparin vs Enoxaparin in patients undergoing microvascular head and neck reconstruction, analyzing the incidence of flap thrombotic complications and local bleeding that could compromise the flap survival. This is an observational study on a group of 204 patients who underwent a microvascular flap for head and neck reconstruction at the Oral and Maxillofacial Surgery Department of Ramon y Cajal Hospital in Madrid, Spain. A group of 67 patients was treated according to a protocol for postoperative prophylaxis of thromboembolism with Bemiparin, which was compared with data collected retrospectively from a group of 137 patients treated with Enoxaparin. We evaluated the incidence of thrombotic complications in the microvascular anastomoses and the incidence of postoperative bleeding events. The flap success rate was 91% in patients treated with Bemiparin, and 91,2% in the group of Enoxaparin (p = 0.963). One major bleeding event was recorded in the Bemiparin group, while 18 events were observed in the Enoxaparin group (p=0.008). Only the type of thromboprophylactic treatment (Bemiparin vs Enoxaparin) was related to presenting major bleeding (p = 0.007). Therefore, Bemiparin is useful in the thromboembolic prophylaxis in patients with microvascular head and neck reconstructions, providing a lower risk of major bleeding than Enoxaparin.