SNPs on LDL-C and coronary heart disease (CHD) was examined in Pakistani subjects and was compared with middle aged UK men from Northwick Park Heart Study II (NPHSII). One thousand nine hundred sixty-five (1770 non CHD, 195 CHD) UK and 623 (219 non CHD, 404 CHD) Pakistani subjects were enrolled in the study. The SNPs SORT1 rs646776, APOB rs1042031 and APOE rs429358, rs7412 were genotyped. The SNPs show a dose response association with LDL-C levels and risk of CHD in both populations. For the APOE polymorphisms, rs429358 and rs7412, isoforms epsilon2, epsilon3 and epsilon4 were examined separately. When compared with epsilon3, epsilon2 lowered LDL-C while epsilon4 raised LDL-C in all the study groups.