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Patients undergoing free tissue transfer are particularly susceptible to hypothermia. The goal was to investigate the impact of intraoperative core body temperature on free flap thrombosis. Two hundred twelve cases of free flap reconstruction at Yale-New Haven Hospital between 1992 and 2008 were reviewed. Free flap thrombosis was defined by complete flap necrosis or direct visualization of arterial or venous thrombosis. Temperature measurements were calibrated to bladder temperatures as measured by Foley catheter sensor. Through logistic regression analysis, maximum and minimum intraoperative temperatures were determined to be statistically significant predictors of free flap thrombosis. The optimal temperature was calculated to be 36.2°C, and maximum intraoperative temperatures between 36.0°C and 36.4°C showed lower thrombosis rates than superwarmed patients (p < 0.03). Therefore, free flap patients should be mildly hypothermic at 36.0°C to 36.4°C, compared with normothermia at 37.5°C, as measured in the bladder. A prospective randomized trial investigating thrombosis rates and intraoperative temperature should be undertaken.