The objective of this study was to identify risk factors for free flap failure among various anatomically based free flap subgroups. The 2005 to 2012 American College of Surgeons National Surgical Quality Improvement Program database was queried for patients undergoing microvascular free tissue transfer based on current procedural terminology codes. Univariate analysis was performed to identify any association between flap failure and the following factors: age, gender, race, body mass index (BMI), diabetes, smoking, alcohol use, hypertension, intraoperative transfusion, functional health status, American Society of Anesthesiologists class, operative time, and flap location. Factors yielding a significance of P < 0.20 were included in multivariate logistic regression models in order to identify independent risk factor significance for flap failure. Furthermore, patients were stratified based on recipient site (breast, head and neck, trunk, or extremity), and analysis was repeated in order to identify risk factors specific to each location. A total of 1921 of 2103 patients who underwent microvascular free flap reconstruction met inclusion criteria. Multivariate logistic regression identified BMI (adjusted odds ratio [AOR] = 1.07, P = 0.004) and male gender (AOR = 2.16, P = 0.033) as independent risk factors for flap failure. Among the "breast flaps" subgroup, BMI (AOR = 1.075, P = 0.012) and smoking (AOR = 3.35, P = 0.02) were independent variables associated with flap failure. In "head and neck flaps," operative time (AOR = 1.003, P = 0.018) was an independent risk factor for flap failure. No independent risk factors were identified for the "extremity flaps" or "trunk flaps" subtypes. BMI, smoking, and operative time were identified as independent risk factors for free flap failure among all flaps or within flap subsets.