Lipoprotein(a) [Lp(a)] is a quantitative genetic trait in human plasma associated with atherothrombotic disease. The major determinant of Lp(a) concentration is the apolipoprotein(a) [apo(a)] gene locus. Variation in the number of kringle IV repeats (K-IV VNTR) in apo(a) has a direct effect on Lp(a) concentrations but explains only a fraction of the large intra- and inter-population variance in Lp(a) levels. Effects on Lp(a) of other intragenic polymorphisms including a pentanucleotide repeat (PNRP) in the promoter likely reflect allelic associations with as yet unidentified sequence variation in the apo(a) gene. We have studied a candidate C-->T transition in two European and two African populations. This polymorphism in the 5' region of the apo(a) gene creates an ATG start codon thereby reducing apo(a) translation in vitro by 60%. All samples were also analyzed for the K-IV VNTR and the PNRP to stratify for their effects and to consider allelic associations. Consistent with the in vitro effect the C-->T transition was associated with a significant reduction in Lp(a) levels in both African populations ( P < 0.0056). In Caucasians, however, the effect was not significant. This was explained by linkage disequilibrium of the +93 T with apo(a) alleles of intermediate length (K-24-K-34) and with nine PNRs. In Europeans these alleles are associated with low Lp(a) which makes any potential effect of the +93 T undetectable in the total sample. From our results we conclude (i) that the +93 C/T polymorphism is the second known intragenic apo(a) polymorphism which affects Lp(a) levels directly in vivo ; (ii) that allelic associations may mask the effect of a mutation; and (iii) that heterogeneity of an effect of a mutation across populations does not disprove causality.