To understand the factors contributing to the synthesis of human apolipoprotein AI (apoAI), relative apoAI synthesis was measured from endoscopic biopsy samples obtained from 18 healthy volunteers. The relative amount of apoAI synthesis was directly correlated with steady state intestinal apoAI mRNA levels and a 10-fold within-group variability was observed. Analysis of genomic DNA from the subjects revealed five polymorphic sites which defined two haplotypes in the intestinal enhancer region of the apoAI gene located upstream of the apolipoprotein CIII gene transcriptional start site (+ 1): (-641 C to A, -630 G to A, -625 T to deletion, -482 C to T, and -455 T to C). The population frequencies of the wild-type and mutant alleles were 0.53 and 0.44, respectively. Mean steady state apoAI mRNA levels and mean relative apoAI synthesis were 49 and 37% lower, respectively, in homozygotes for the mutant allele and 28 and 41% lower, respectively, in heterozygotes than in homozygotes for the wild-type allele (P < 0.05 for both). Site-directed mutants of apoAI gene promoter/reporter constructs containing the above mutations were transfected into Caco-2 cells and showed a 46% decrease in transcriptional activity compared with the wild type (P < 0.001); however, no significant differences were observed in HepG2 cells. Electrophoretic mobility shift assays showed that the mutated sequences from -655 to -610 bound Caco-2 cell nuclear protein(s) while the wild type did not. These results indicate that intestinal apoAI gene transcription and protein synthesis are genetically determined and are reduced in the presence of common mutations which induced binding of nuclear protein(s), possibly a transcriptional repressor.