Thrombotic and thromboembolic events are important causes of mortality and morbidity in patients with prosthetic heart valve. The aim of this study is to evaluate the factors that may contribute to prosthetic heart valve thrombosis. This was a cross-sectional study in Rajaie Heart Center on patients with prosthetic heart valve malfunction, within a year. According to the echocardiographic and fluoroscopic findings, the patients were divided into two groups (thrombosis and non-thrombosis groups). The patients' demographic, clinical and laboratory data were recorded and analyzed with SPSS software. A total of 142 patients participated in this study. Ninety-four patients (66.2%) were diagnosed with thrombosis. There was a significant relationship between thrombosis and inadequate anti-coagulation (international normalized rati [INR] <2.5) (odds ratio [OR]: 4.15, 95% CI: 1.98-9.87, P = 0.003), history of infection (OR: 12.81, 95% CI: 3.52-19.02, P<0.001), prothrombin time (PT) check interval (OR: 2.38, 95% CI: 1.63-8.47, P = 0.019), atrial fibrillation (AF) rhythm (OR: 3.96, 95% CI: 1.75-8.09, P = 0.019), and plasma fibrinogen level (OR: 6.90, 95% CI: 2.58-14.69). Based on this study, inadequate anti-coagulation, AF rhythm, recent infection and plasma fibrinogen level were the factors most contributing to prosthetic valve thrombosis. As there were many cases of thrombosis in patients with history of infection, this factor can be considered for risk assessment in prosthetic valve.