Antimicrobial peptides are important components of host defenses against microbial invasions. Bactericidal permeability-increasing protein (BPI) is an antimicrobial peptide belonging to the lipid transfer/LPS-binding protein family. It serves important roles in defending against Gram-negative bacteria in the innate immune system. Here we report cloning of complete BPI cDNA from channel catfish (Ictalurus punctatus) by 5' RACE after obtaining the partial BPI cDNA sequence from EST analysis. The channel catfish BPI cDNA is 1640 bp in length with a 1428-bp open reading frame that encodes a protein of 475 amino acids. Catfish BPI gene shows high similarity with the BPI/LBP gene isolated from other teleost fish. As part of ongoing efforts in comparative genome analysis, we have assigned the catfish BPI gene to bacterial artificial chromosome (BAC) clones. Southern blot analysis on multiple BPI BAC clones indicated the presence of a single copy of the BPI gene in the catfish genome. Reverse transcription-polymerase chain reaction (RT-PCR) analysis on healthy tissues showed that BPI was expressed in a wide range of tissues including head kidney, gill, skin, trunk kidney, brain, intestine, liver, muscle, ovary, spleen and stomach. The BPI gene was not developmentally expressed until 48 h after fertilization. Quantitative real time PCR (QRT-PCR) analysis indicated that the BPI gene expression was induced after challenge with Edwardsiella ictaluri, the causative agent of enteric septicemia of catfish (ESC). BPI upregulation peaked 3 days after challenge, mirroring the expression pattern of inflammatory chemokines in catfish, suggesting that it plays a role in the innate defense response.