To investigate the mechanisms controlling tissue-specific expression of the human apolipoprotein (apo) E/C-I gene locus, human apoE and apoC-I gene constructs containing various lengths of the 5'-flanking or 3'-flanking region were used to create transgenic mice. Several essential tissue-specific regulatory elements were identified in the region between the apoE and the apoC-I genes, as well as in a distal domain found downstream of the apoC-I gene. Most notably, transcription of both the apoE and apoC-I genes in the liver, their major site of expression, required downstream regulatory elements, possibly located within a common regulatory domain more than 2 kilobases 3' of the apoC-I gene (about 14 kilobases downstream of the apoE gene promoter). In the region between the apoE and apoC-I genes, a single strong positive element directed apoE and apoC-I gene expression in the skin. The intergenic region also contained elements that stimulated apoE gene expression in the brain and silenced apoE gene expression only in the kidney. These results demonstrate that multiple independent regulatory elements control expression of the human apoE/C-I gene locus in various tissues. Transgenic mice expressing human apoC-I in the liver exhibited plasma triglyceride levels that were 2-3-fold higher than those in control mice, an effect not found when transgenic human apoE was produced. This result suggests that apoC-I may modulate the metabolism of triglyceride-rich lipoproteins.