BACKGROUND Because of the low incidence of late thrombosis in free flaps used for head and neck reconstruction, the risk factors, prognosis, and the optimal method of treatment are unclear. METHODS The timing of thrombosis, types of flaps, occluded vessels, causative factors, previous irradiation, and salvage rates were reviewed and compared between 79 patients who had thrombosis on postoperative day 4 or earlier (early-thrombosis group) and 24 patients who had thrombosis on postoperative day 5 or later (late-thrombosis group). RESULTS The main causative factor for thrombosis in the late-thrombosis group was wound infection (54%), whereas wound infection was present in only 1% of cases of thrombosis in the early-thrombosis group. None of the flaps could be salvaged in the late-thrombosis group. CONCLUSIONS Poor salvage rate in the late-thrombosis group is the most serious problem. Prevention, early detection, and appropriate management of wound infection are essential for avoiding late thrombosis.