Mechanical valve malfunction due to thrombosis is an important and life-threatening complication in patients with prosthetic valves. Our study was performed to determine the prevalence of thrombophilia genes among patients with acute thrombosis of the mechanical pulmonary valves despite acceptable anticoagulation levels. In this cross-sectional comparative study thirthy two consecutive patients with acute thrombosis of pulmonary mechanical valve who had international normalized ratio (INR) levels for prothrombin time of at least 2 at the time of presentation and in the preceding three months were enrolled and the prevalence rates of thrombophilia factor genes among them was assessed. The results showed that 24 patients (75%) had thrombophilia gene mutations. The affected patients had mutations in one gene in 37.5% of cases, two genes in 31.3%, and three genes in 6.3%. Prevalence rate of Factor V Leiden (FVL), prothrombin (PTH), Plasminogen activator inhibitor-1 (PAI-I), Methylenetetrahydrofolate Reductase (MTHFR), and endothelial protein C receptor (EPCR) gene mutations was 3.1%, 6.3%, 50%, 37.5%, and 25%, respectively. In our study the prevalence of thrombophilia factor gene mutations of patients with acute thrombosis of pulmonary valve was higher than that reported in the general population.