We characterized genes for prophenin (PF)-2 and PR-39, two cathelin-associated antimicrobial peptides found in porcine leukocytes. Both contained 4 exons and 3 introns and were compact, contiguous and highly homologous. Exons I-III encoded most of their cathelin domains. Exon IV specified the final few cathelin residues, including its conserved C-terminal valine, followed by the mature PR-39 peptide or a PF-2 precursor. The highly conserved 5' flanking sequences of this gene family contained NF-kappa B, IL-6, GM-CSF and NF-1 binding motifs and the introns were unusually conserved. These data suggest that the panoply of porcine cathelin-associated antimicrobial peptides arose relatively recently via gene reduplications and exon shuffling, and that in vivo expression of cathelin-associated antimicrobial peptides may respond to mediators generated early during infection.