AIM: To study the distribution of C46T polymorphism of factor Ⅻ(FⅫ) in Chinese Han population and the association of the polymorphism with coronary artery disease(CAD) and acute coronary syndrome(ACS). METHODS: Selected coronary angiography was performed in 168 CAD patients and 210 controls. Genetype of FⅫ was typed by mutagenically separated polymerase chain reaction assay(MSPCR). RESULTS: FⅫ allelic frequencies of C and T were 29.8%, 70.2% and 31.4%, 68.6% in CAD and controls, respectively(P>0.05). Genetype distribution was in accordance with Hardy-Weinberg equilibrium. The frequency of CC, CT, TT in CAD and control was 8.7%, 40.5%, 50.0% and 5.2%, 52.6%, 42.2%. The association between FⅫ genetype and CAD(χ~2=6.393, P<0.05) was observed. As compared with the CC group, the CT genetype was a protective factor for CAD(OR 0.43, 95% CI 0.19-0.97). When compared to stable coronary artery disease, the frequency of TT genetype is significant less in ACS group(45.0% vs 62.5%, χ~2=4.200, P<0.05). The distribution of genetype in C46T was no significant difference among the numbers of stenosed coronary artery. CONCLUSION: The C46T polymorphism of FⅫ is association with CAD in Chinese Han population. The C→T mutation may be a protective factor against CAD and ACS.