The aim of this study was to investigate the association between apolipoprotein B gene polymorphisms and coronary artery disease and lipid levels in north Indians. Two hundred patients of angiographically proven atherosclerotic CAD and two hundred age and sex matched control subjects were included in the study. Serum lipids including cholesterol, triglycerides, HDL, LDL, VLDL and ApoB were analyzed. PCR based genotyping was done for ApoB 3' Hypervariable region (HVR). RFLP analysis was carried out to genotype regions carrying XBA1, EcoR1 and Msp1 restriction sites in the ApoB gene. Biochemical analysis of lipid parameters revealed that Total cholesterol, triglycerides, VLDL, LDL and ApoB were significantly high (p 37) were significantly (p 37) of ApoB3'HVR and E+/X- RFLP haplotype is strongly associated both with elevated lipid levels and CAD occurrence. Therefore, ApoB gene polymorphisms can be helpful in delineating the high risk group for CAD and may be of use in genetic screening of CAD patients from north India.