The underlying genetic abnormalities in familial combined hyperlipidemia (FCH) have not been elucidated, although previous association and linkage studies have implicated the apoA-I/C-III/A-IV gene cluster. We now report studies of this cluster in 18 probands, 390 family members (hyperlipidemic relatives, n = 179; normolipidemic relatives, n = 211), and 177 spouses. Three restriction enzyme polymorphisms, XmnI and MspI sites 5' of the apoA-I gene and the SstI site in the 3' untranslated region of exon 4 of the apoC-III gene, were examined. In hyperlipidemic relatives and FCH probands, the frequency of each minor allele was significantly higher than in spouses. Associated with the higher frequency of minor alleles were elevated plasma cholesterol, triglycerides, LDL-cholesterol, apoB, and apoC-III levels. Quantitative sib-pair analysis revealed linkage between the MspI minor allele and plasma LDL cholesterol levels (P < 0.04). The present data indicate that, while apoA-I/C-III/A-IV gene cluster is not the primary cause of FCH, this cluster has a specific modifying effect on plasma triglyceride and LDL cholesterol levels.