Cathelicidins are antimicrobial peptides present in humans, and laboratory and domestic animals. These peptides are essential components of innate and acquired immune responses; however, little is known about cathelicidin gene regulation. To investigate the regulatory mechanisms of cathelicidin gene expression, we characterized the promoter of the PR-39 gene, a multifunctional cathelicidin. Deletion analysis identified a negative regulatory element in the 5'-flanking region of the gene located in the sequence from nt (nucleotide(s)) -69 to -63. Site-directed mutagenesis indicated that ATG and its vicinity nucleotides are critical for the repressive activity of this region. A primer extension assay identified a transcription start site upstream from the negative repressor ATG and 76 nt upstream from the major open reading frame (ORF). RT-PCR and 3'-RACE further demonstrated that cDNA of PR-39 and the cathelicidin porcine myeloid antimicrobal peptide (PMAP)-23, which share prepro sequence identity, start from nt -79. Sequencing of this region showed that the 5' untranslated region (UTR) of the gene contains an upstream translation start site and an upstream ORF that functions as a repressor of the PR-39 gene. These findings indicate extensive regulation of the PR-39 gene and suggest a mechanism for the tissue-specific and age-dependent repression of this cathelicidin gene.