Two polymorphic sites of the apolipoprotein AI (ApoAI) gene, PstI and SstI, were examined in a sample of 43 unrelated Chinese patients with coronary artery disease (CAD) and 60 unrelated healthy individuals. Allele frequencies were compared between patients and controls and their impact on lipid and oxygen free radicals metabolism were also studied. The frequencies of the uncommon P2 and S2 alleles in CAD cases were found as 0.14 and 0.22 respectively, which were significantly higher than 0.05 and 0.13 in controls. The more the number of vessel disease in CAD cases, the higher the frequencies of S2 alleles which were the highest in the group of 3 vessel diseases. Some serum lipid and oxygen free radicals levels differed between CAD cases of different genotypes. These data suggest that genetic variation in P2 and S2 alleles of APOAI gene may contribute to the development and extent of CAD in Chinese subjects.