A mutation in coagulant factor V gene, a substitution in the 3' untranslated region of prothrombin gene, and a variant in 5,10-methylenetetrahydrofolate reductase (MTHFR) gene have been reported to be related to venous thromboembolism in Caucasians, but this relationship remains in debate in other populations. In this case-control study, we aimed to determine the prevalence of these three mutations in the Chinese population and investigate whether they are associated with pulmonary thromboembolism. The subjects consisted of 90 patients with pulmonary thromboembolism and 143 age- and sex-matched healthy controls. Traditional risk factors for venous thrombosis and pulmonary thromboembolism were investigated as well. We found that the frequencies of varicose vein, phlebitis, trauma, and surgery were significantly higher in cases than in controls. Of all subjects, none was a carrier of coagulant factor V gene G1691A mutation or prothrombin gene G 20210A mutation, which are common point mutations in Caucasians, while the frequency of MTHFR gene 677T allele exceeded 55% in cases (56.7%), controls (55.2%), and all subjects (55.8%) studied. The homozygous mutation rate of MTHFR gene was over 30% in both cases (33.3%) and controls (32.2%), but no significant difference was found in genotype distribution (chi(2)=0.100, P=0.951). Model fitting using logistic regression did not find that MTHFR gene C677T mutation was associated with pulmonary thromboembolism, consistent with the results of stratification analysis. In conclusion, coagulant factor V gene G1691A mutation and prothrombin G20210A mutation are very rare, while MTHFR C677T mutation is very common, and all of them are not associated with pulmonary thromboembolism in the Chinese population.