Systemic-pulmonary shunts are widely used in initial palliation in cyanotic congenital heart disease. The incidence and the relationship between acute shunt obstruction and thrombophilia are not precisely defined. The aim of this study was to determine the frequency of shunt obstruction in the early postoperative period, and to define the frequency and presence of thrombophilia factors in patients treated for acute shunt thrombosis. Between October 2010 and October 2012, 77 patients who had systemic-pulmonary shunt operation were included in this prospective study. Patients who developed shunt obstruction were examined in terms of inherited and acquired thrombophilia factors. Median patient age was 61 days and median weight was 4.3 kg. Thirty-three patients were neonates. Diameter of the Gore-Tex grafts used for the shunt ranged from 3 mm to 5 mm. Acute shunt occlusion rate was 10% (8/77), and all of these occurred in the first 24 h. Thrombophilia was found in three of eight patients who underwent intervention (surgical and/or transcatheter) due to shunt thrombosis (presence of anti-phospholipid antibodies, n = 1; protein C deficiency, n = 1; and factor V Leiden mutation, n = 1) and only one patient died. Acute shunt obstruction developed in 10% of patients who underwent systemic-pulmonary shunt, and emergency surgery or transcatheter intervention can be life saving in this context. Acute shunt obstruction can occur due to mechanical and hemodynamic problems, but clinicians should also consider and evaluate thrombophilia factors.