Insertion/deletion (Ins/Del) polymorphism of the apo B gene encoding signal peptide and its relation to coronary heart disease (CHD) and lipid trait were studied in 103 patients with CHD and 100 healthy individuals from Chinese Han nationality. The frequency of rare Del allele was 0.259, which was significantly lower than 0.34 in Caucasians (France), but higher than 0.16 in South Asian descents in UK. When the frequency distribution of the Ins/Del alleles was compared between CHD group and control group, the frequency of rare Del allele in the patient group was not apparently different from that in the control group (0.282 vs. 0.235, P > 0.05). As for the impact of the Ins/Del genotype on levels of lipid and apolipoprotein, the patients with at least one Del allele had significantly lower HDL-C level compared with those with only Ins allele in the CHD group (P < 0.01). Levels of other lipid parameters in each group were not obviously associated with the Ins/Del genotype. It is suggested that the Ins/Del polymorphism of the apo B signal peptide might be involved in lipid metabolism by an unidentified mechanism in some ethnic population. PCR is a useful method for distinguishing Ins/Del polymorphism of the apo B signal peptide.