Like humans, baboons possess apolipoprotein[a] (apo[a]), a unique protein component of the atherogenic lipoprotein [a] (Lp[a]) particle. Baboon apo[a] also exhibits extensive variation with respect to size and serum levels. In this report, we have cloned the 5' flanking region of the baboon apo[a] gene (I isoform) and performed promoter mapping studies to identify sequences that control apo[a] transcription. The sequence of the baboon apo[a] 5' flanking region is similar to the human gene, and contains two Alu repeats that distinguish the apo[a] gene from plasminogen and other apo[a]-like genes. The transcription start site for the baboon apo[a]gene is located 85 bp upstream from the major start site for the human apo[a] gene. For promoter mapping studies, we constructed two sets of deletion clones (5' to 3' and 3' to 5') in luciferase reporter plasmids for transfection of hepatic cell lines (HepG2 and HUh7). These experiments showed that the 5' untranslated region (5' UTR) contains a positive promoter element with 85% identity to the consensus binding site for hepatocyte nuclear factor 1 alpha (HNF-1 alpha), and a negative element that is functional in HepG2 cells, but not Huh7 cells. Transfection assays with HeLa cells showed that the positive promoter element acts in an hepatocyte-specific manner. We also cloned the 5' flanking region from a baboon carrying a null allele that produced no detectable hepatic transcripts or serum isoforms in vivo. Surprisingly, the 5' flanking regions of the null allele possessed a promoter that was functional in transfection assays. We conclude that the baboon apo[a] gene 5'UTR contains hepatocyte-specific promoter elements, but that other unknown sequences must influence apo[a] expression in vivo.