Background: Despite excellent results from free flap transfers, postoperative thrombosis does occur and, although infrequent, causes total loss of the flap. We investigate the risk factors of anastomotic thrombosis in head and neck free flaps. Study Design, Subjects and Methods: A retrospective analysis was carried out on 200 consecutive free flaps applied to patients who underwent head and neck reconstruction. Multiple logistic regression analysis was conducted to identify risk factors of anastomotic thrombosis, taking into account twelve factors: diabetes, obesity, hypertension, hypertriglyceridemia, proteinuria, age, gender, smoking habit, habitual alcohol intake, previous chemotherapy and radiation, and hypercholesterolemia. Results: Hypertension, female gender, aging, and drinking habit were statistically significant risk factors of postoperative thrombosis. Conclusions: Our data suggest that four factors mentioned above are possible predictors of anastomotic thrombosis in free flaps used for head and neck.