We have previously shown that high density lipoprotein is the most abundant protein in the carp plasma and displays bactericidal activity in vitro. Therefore the aim of this study was to analyze the contribution of its principal apolipoproteins, apoA-I and apoA-II, in defense. Both apolipoproteins were isolated by a two step procedure involving affinity and gel filtration chromatography and were shown to display bactericidal and/or bacteriostatic activity in the micromolar range against Gram-positive and Gram-negative bacteria, including some fish pathogens. In addition, a cationic peptide derived from the C-terminal region of carp apoA-I was synthesized and shown to posses antimicrobial activity (EC50 = 3–6 μM) against Planococcus citreus. This peptide was also able to potentiate the inhibitory effect of lysozyme in a radial diffusion assay at subinhibitory concentrations of both effectors. Finally, limited proteolysis of HDL-associated apoA-I with chymotrypsin in vitro was shown to generate a major truncated fragment, which indicates that apoA-I peptides liberated in vivo through a regulated proteolysis could also be involved in innate immunity.