Thrombosis of the arterial microanastomosis is the major reason for flap complications. Thrombus formation can occur rapidly at the site of anastomosis, or it may be delayed in developing, inducing secondary ischemia. The damaged endothelial cells and the exposed connective tissue play an important role in the molecular and cell mechanisms of coagulation and thrombosis. For this reason the early morphological changes in the endothelial cell layer after arterial microanastomoses in the rat were investigated. The results showed that the anastomotic site appeared completely sealed, with cut ends protruding into the vessel lumen. Extensive deendothelialized areas with fibrin deposition were visible between surgical microclamps on the inner surface of the artery. For this reason we believe that the damaged endothelium and exposed connective tissue elements are the primary cause of thrombin formation, platelet accumulation, and thrombosis at the anastomotic site. The reconstructive surgeon must employ a very meticulous microvascular technique to minimize damage to the vascular endothelium.