The transverse rectus abdominis muscle flap is widely used in free microvascular tissue transfer for breast reconstruction following mastectomy. Flap survival may be compromised by failure at the microsurgical anastomosis due to both venous and arterial thrombosis. It is unclear, whether hereditary thrombophilia represents a risk factor for early thrombotic occlusion following free flap procedures. We present a case of a patient with previously diagnosed activated protein resistance caused by heterozygous factor V (position 1691 G-->A) Leiden mutation in whom a free transverse rectus abdominis muscle flap was performed. The postoperative course was complicated by repeated thrombosis of both the venous and arterial part of the anastomosis. Immediate thrombectomy and repeated arteriography allowed for partial flap salvage. More data are needed to analyze the impact of hereditary thrombophilia on microvascular anastomosis failure.