In view of the clinical importance of apolipoprotein B (apo B) as a major risk factor for coronary artery disease (CAD), we investigated the two polymorphisms (signal peptide and XbaI) of the apo B gene in 235 Korean patients with CAD and in 216 normal controls. The insertion allele (INS) frequency of signal peptide polymorphism was significantly higher in cases than the controls (P<0.05). Signal peptide polymorphism was also associated with levels of plasma cholesterol, triglyceride and low density lipoprotein-cholesterol. However, XbaI polymorphism was not associated with plasma lipid levels. Therefore, our results suggest that signal peptide polymorphism of the apo B gene might be one of the factors in explaining an association in Korean CAD patients.