Two polymorphic sites of apolipoprotein B (apoB) gene, XbaI and EcoRI, were examined in 80 patients with documented coronary heart disease (CHD) and 60 healthy individuals selected from a population of Chinese Han nationality. Allele frequencies at these sites were compared between the patients and controls and their impact on lipid metabolism was also investigated. The frequency of X+ allele (presence of XbaI cutting site) in CHD patients was 0.10, which was significantly higher than 0.01 in controls (P < 0.001). The same trend was detected for frequency of E-allele (lack of EcoRI cutting site) when it was compared between CHD patients and controls (0.11 vs 0.05), the difference was not statistically significant (P < 0.1, > 0.05). There was no relationship between XbaI RFLP and EcoRI RFLP. In the CHD patients, X+ allele was associated with the lower levels of HDL-C and apoAI when compared with X- allele, while no associations were found of X+ allele with other lipid parameters. On the contrary, the EcoRI polymorphism had no significant influence on plasma lipid and lipoprotein levels. Therefore, it was suggested that genetic variation at XbaI site of apoB gene might contribute to the determination of plasma HDL-C level and development of CHD in people among Chinese Han nationality.