Abstract An Hpa I restriction site located 317 bp upstream of the transcription initiation site of the apoC-I gene has been shown to increase apoC-I gene transcription in vitro. The aim of the present study was to determine whether this genetic polymorphism was associated in vivo with increased plasma levels of apoC-I. In a cohort of French–Canadians ( n=391) recruited for a family study, we found strong linkage disequilibrium between the genes for apoC-I and apoE (as reported before for European–Americans), such that the apoC-I Hpa I-negative (H1) allele was strongly associated with apoE ε3, whereas the apoC-I Hpa I-positive (H2) allele was strongly associated with apoE ε2 and ε4. ApoC-I and apoE were measured by ELISA in total plasma and in very low-density lipoproteins (VLDL) separated by ultracentrifugation (d<1.006 g/ml), and then by difference for the non-VLDL fraction (d>1.006 g/ml), in a subset of families selected for their diverse apoE genotypes. Subjects were divided into normolipidemic (NL, n=89, TG<2.3 mmol/l, LDL-C<3.8 mmol/l) and hyperlipidemic groups (HL, n=88, TG>2.3 mmol/l and/or LDL-C>3.8 mmol/l). In NL subjects, apoC-I levels were not significantly associated with apoC-I genotype (H1/H1, H1/H2 or H2/H2). They were, however, related to apoE genotype, such that apoE3/2 subjects tended to have higher and apoE4/3 subjects tended to have lower concentrations of total plasma and non-VLDL apoC-I and apoE. Total plasma, VLDL and non-VLDL apoC-I and E levels were also higher in HL subjects with an apoE2/2 or apoE3/2 genotype. These results suggest that plasma levels of apoC-I are more strongly influenced by apoE genotype than by the Hpa I apoC-I promoter polymorphism, which probably reflects an effect of different apoE isoforms on plasma lipoprotein and plasma apoC-I metabolism, rather than a direct effect of apoE alleles on apoC-I transcription.