The cutaneous barrier contains small, cationic antimicrobial peptides that participate in the innate immunity against a wide variety of pathogens. Despite their immune importance, knowledge of canine defensins and their expression is limited primarily to testicular tissue and their relation to coat colour. Studies have shown that the absence of these antimicrobial peptides contribute to increased secondary infections in humans. The goals of this study were to identify defensin and protease inhibitor peptide genes by performing a computer-based iterative screen of the canine genome and to determine whether antimicrobial peptides are expressed in normal canine skin. Reverse transcription-polymerase chain reaction (RT-PCR) was used to test for the expression of several antimicrobial peptides in the skin of five normal dogs. RNA from testis was used for comparison. The iterative screen identified 65 putative antimicrobial peptide genes on nine chromosomes, the majority clustered on chromosomes 16 and 24. Amplification of normal canine skin cDNAs demonstrated expression of antimicrobial peptide genes in five different body sites. These findings will provide a tool for future studies examining the association between antimicrobial gene expression and cutaneous immunity in dogs.