Four polymorphic sites of the apolipoprotein B (apo B) gene were investigated by using polymerase chain reaction (PCR) in 103 patients with coronary heart disease (CHD) and 100 age-matched healthy individuals selected from a population of Han Chinese in the Beijing area. The rare X+ allele of the XbaI restriction site was more frequently seen in CHD patients than in controls (0.088 vs. 0.025, P < 0.01). The relative frequency of rare E- allele of the EcoRI restriction site was significantly higher in CHD patients compared with controls (0.11 vs. 0.04, P < 0.01). Similarly, 3'VNTR-L allele (number of repeat units > 39) at the VNTR region was also present at an apparently high frequency in CHD patients in comparison to that in controls (0.602 vs. 0.290, P < 0.001). However, the difference in relative frequency of rare Del allele of the Ins/Del polymorphism at the signal peptide was not significant between the two groups (0.282 vs. 0.235. P > 0.05). In comparison with Caucasians, the relative frequencies of rare alleles (Del, X+ and E-) were found to be statistically lower in Han Chinese. Furthermore, the Del and X+ alleles, in linkage disequilibrium, were associated with significantly lower plasma level of HDL-C in CHD patients. Therefore it is suggested that genetic variation with the apo B gene may exert some impact on lipid metabolism and contribute to the susceptibility to development of CHD in Han Chinese.