Pulmonary embolism is usually considered as a complication of deep vein thrombosis, but there are still a number of cases of isolated pulmonary embolism. We aimed to investigate whether prothrombin 3'end gene variants might play a significant role in the pathogenesis of isolated pulmonary embolism.In this study 100 patients with isolated pulmonary embolism and 100 controls were screened by DNA sequencing. Screening included last intron, last exon, 3'UTR and part of the 3'FR region of the prothrombin gene. Our results have shown that heterozygous carriers of the FIi G2021 OA variant have a significantly higher risk of isolated pulmonary embolism (OR 4.83; 95% CI 1.33-17.52; P=0.02). Carriers of the Ili 19911GG genotype (OR 1.41; 95% CI 0.72-2.73; P=0.31) and FII 20068CT genotype (OR 3.06; 95% CI 0.31-29.95; P=0.34) were more frequent in patients with isolated pulmonary embolism compared to controls. We also detected the novel gene variants, FIIc.*64_*66del and FII c.*303T>C, in two patients.Our results suggest that FII G20210A represents a significant risk factor for isolated pulmonary embolism. The FII G19911A and FII C20068T are potentially associated with an increased risk for the occurrence of isolated pulmonary embolism, but the results did not reach statistical significance. This is the first study in which the two novel 3'end prothrombin gene variants, FIIc.*64_*66del and FlI c.*303T>C, were reported.