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Pulmonary thromboembolism (PTE) is a common clinical problem that is associated with substantial morbidity and mortality. We investigated the role of protein C polymorphism in patients with PTE in order to find out the correlation between its polymorphism and the susceptibility of the Chinese population to develop PTE. We used a case-control study design. Sixty-three consecutive patients with PTE were enrolled as the investigated group and 86 healthy people as the control group. Two novel polymorphisms, C/T at the position of 2405 and A/G at the position of 2418in the protein C gene promoter region were detected through PCR-restriction fragment length polymorphism analysis. The results suggested that the genotype frequencies of the two single-nucleotide polymorphisms (SNPs) when combined together were not significantly different between the case and control group (P > 0.05). However, the allele frequency of the C2405T SNP was significantly different between the case and control group. The frequency of T allele in the PTE group was higher when compared to the control, whereas the frequency of C allele was lower (P < 0.05). These results suggested that there were six different kinds of genotype distribution (TA-TA, TA-CA, TA-CG, CG-CG, CA-CG, CA-CA) and three different kinds of haplotype (TA, CG, CA). Our result showed that the frequency of the TA haplotype was significantly higher in the patients suffering from PTE (P < 0.05). These results suggest that the two polymorphisms present in the control region of the protein C gene are associated with an increased susceptibility to PTE in the Chinese population. The 2405T allele may be a possible risk factor for the development of PTE, whereas the C allele may probably be a protective factor of PTE Moreover, the TA haplotype may also be associated with an increased risk for developing PTE.