Background Deep venous thrombosis (DVT) can result in pulmonary embolism, a fatal complication that is due to the dislodgement and movement of a blood clot (thrombus) from a limb into the lungs. Genetic risk factors related to DVT development include mutations in coagulation proteins, especially the endothelial protein C receptor (EPCR), a component of the anticoaguiation protein C (PC) pathway. The objective of the present study was to analyze the relationship between the 6936A/G polymorphism in the EPCR gene and the occurrence of DVT.Methods This study involved 65 patients with DVT and 71 age- and gender-matched healthy controls. Peripheral blood samples were collected from all subjects. Plasma levels of soluble EPCR (sEPCR) were measured by enzyme-linked immunosorbent assay. Genomic DNA was extracted and EPCR gene product was amplified by a standard PCR reaction.Gene product bands were sequenced to identify EPCR gene polymorphisms.Results In the control group, the level of sEPCR in subjects with 6936AG genotype was significantly higher than that in subjects with 6936AA genotype ((0.97±0.32) pg/ml vs. (0.61±0.24) pg/ml, P ＜0.01). Similarly in the DVT group, the level of sEPCR in subjects with the 6936AG were greater than that in subjects with the 6936AA genotype ((0.87±0.21) pg/ml vs. (0.50±0.18) pg/ml, P ＜0.01). The sEPCR level in DVT patients was significantly higher than that in healthy controls ((0.68±0.32) pg/ml vs. (0.54±0.22) pg/ml, P ＜0.05). The 6936AG genotype frequency in DVT patients was significantly higher than that in healthy controls (P ＜0.05). In contrast, the 6936AA genotype frequency in DVT patients was lower than that in healthy controls (P ＜0.05). Subjects carrying 6936AG had an increased risk of thrombosis (OR=2.75, 95% CI:1.04-7.30, P ＜0.05).Conclusions EPCR gene 6936A/G polymorphism is associated with increased plasma levels of sEPCR. Subjects carrying 6936AG likely have an increased risk of thrombosis.