Vascular thrombosis is one of the major postoperative complications of free flap microvascular breast reconstruction operations. It is associated with higher morbidity, higher cost, increased length of hospital stay, and potentially flap loss. Our purpose is to evaluate the rate of this complication and whether patient characteristics play a role. Using the Nationwide Inpatient Sample (NIS) database, we examined the clinical data of patients who underwent free flap breast reconstruction between 2009 and 2010 in the United States. Multivariate and univariate regression analyses were performed to identify independent risk factors of flap thrombosis. A total of 15,211 patients underwent free flap breast reconstruction surgery (immediate reconstruction: 43%). The most common flap was the free deep inferior epigastric perforator (DIEP) flap (53.6%), followed by free transverse rectus abdominis myocutaneous (TRAM) flap (43.1%), free superficial inferior epigastric artery (SIEA) flap (2%), and free gluteal artery perforator (GAP) flap (1.3%). The overall rate of flap thrombosis was 2.4 %, with the highest rate seen in the SIEA group (11.4%) and the lowest in the TRAM group (1.7%). Peripheral vascular disease (adjusted odds ration [AOR] 10.61), SIEA flap (AOR, 4.76) and delayed reconstruction (AOR, 1.42) were found to be statistically significant risk factors for flap thrombosis. Other comorbidities were not linked. While the overall rate of flap thrombosis in free flap breast reconstruction was relatively low (2.4%), Plastic Surgeons should be aware that patients with peripheral vascular disease and those undergoing free SIEA flap are at higher risk of flap thrombosis and they should closely monitor flaps to increase the chance for early salvage.