Concentrations of the lipoprotein Lp(a) vary widely in healthy individuals, but in many studies, high concentrations are strongly associated with cardiovascular disease. On the basis of lipid and protein composition, Lp(a) is a variant of the atherogenic low-density lipoprotein but differs in possessing the unique apolipoprotein(a) [apo(a)]. Lp(a) concentrations are controlled at the level of biosynthesis of the apo(a) protein, which is encoded by the LPA locus, and allelic differences at LPA are responsible for the bulk of variation in Lp(a) phenotype. In this article we describe several aspects of allelic variation at LPA reported in studies of human and baboons, including (1) polymorphisms for protein size, (2) families of alleles having distinct relationships between apo(a) size and Lp(a) concentration, (3) sequence polymorphisms, (4) a group of alleles whose protein products have a multibanded phenotype, and (5) allelic diversity of null phenotype alleles (whose protein products are not detected in the plasma). The data make clear that no single aspect of allelic variation at LPA is sufficient to fully explain the genetic control of Lp(a).