Common variants at the apolipoprotein B gene locus are associated with hyperlipidaemia, but conflicting data have been presented in the literature concerning the size of the effects and which polymorphisms give the best signal in the different groups of individuals studied. In this review, we will present a critique on the use and interpretation of association studies, with respect to the recent apolipoprotein B DNA polymorphism studies. The impact of these common polymorphisms and rare mutations of apolipoprotein B, primarily the substitution of arginine by glutamine at residue 3500 (R3500Q) that causes familial defective apolipoprotein B100, will also be considered.