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Objective 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 signifi cant role in the pathogenesis of isolated pulmonary embolism. Methods and results 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 G20210A variant have a signifi cantly higher risk of isolated pulmonary embolism (OR 4.83; 95%CI 1.33-17.52; P = 0.02). Carriers of the FII 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 gt C, in two patients. Conclusions Our results suggest that FII G20210A represents a signifi cant 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 signifi cance. This is the fi rst study in which the two novel 3’ end prothrombin gene variants, FIIc.*64_*66del and FII c.*303T gt C, were reported.