Linkage and association of the apo AI-CIII-IV gene region to familial combined hyperlipidemia (FCHL) was reported previously, based on the presence of genetic variants in the apo CIII and apo AI gene. No data were available yet on the contribution of the apo A-IV locus. Two DNA variants in exon 3 of the apo A-IV gene, A (Thr)(347)T (Ser) and [CTGT](3-4) were characterized by sequencing the coding region of the apo A-IV gene and were analyzed in our Dutch FCHL cohort (30 probands, 159 affected relative, 317 unaffected relatives and 218 spouses). The genotype frequency of the A(347)T variant was different in probands and spouses. In probands no 2/2 carriers were found, resulting in a significant decreased frequency of the 2-allele (P<0.05). This was suggestive for a protective role of the presence of the serine (T) allele on the prevalence of FCHL. No difference in frequency distribution was found for the [CTGT](3-4) variant between the groups. Homozygous 4/4 carriers in spouses had a more favorable lipid profile (LDL-cholesterol and apo B, P<0.05). The absence of linkage disequilibrium of the A(347)T with other markers in the gene cluster, and the absence of linkage disequilibrium with [CTGT](3-4) marker and the MspI-AI marker in the apo A-I promoter showed that these two apo A-IV variants reside on different haplotypes from the apo A-I and apo C-III markers. This was illustrated by extensive haplotype analysis. The present data on the contribution of DNA variants in the apo A-IV gene support our previous observations that the apo AI-CIII-AIV gene cluster has a complex genetic contribution to FCHL both by conferring susceptibility and protection.