A comparative study was conducted on the antibacterial activities of linoleic acid hydroperoxide (LAHPO) and linoleic acid (LA) against the intestinal bacteria including 35 strains, and the representative species were examined for lipid degradation activity. Enterobacterial species (Escherichia coli, Proteus mirabilis, Citrobacter sp. and Enterobacter sp.), Lactobacillus species (acidophilus, casei and plantarum), and Enterococcus faecalis generally showed the same levels in susceptibility to LA and LAHPO. Bacteroides species (distasonis, vulgatus and thetaiotaomicron) and Clostridium ramosum were highly resistant against LA but not LAHPO. Staphylococcus species (aureus and epidermidis), Lactobacillus species (salivarius and fermentum) and the Grampositive anaerobic bacteria including Clostridium perfringens, Bifidobacterium species (bifidum, infantis, adolescentis, breve, longum, animalis, pseudolongum and thermophilus), Peptostreptococcus productus, and Eubacterium sp. were more susceptible to LAHPO than were the enterobacterial species and E. faecalis although they were more resistant against LAHPO than LA. Eubacterium aerofaciens was more susceptible to LAHPO, but strikingly susceptible to both lipids compared to the other bacterial strains. Thin layer chromatography showed that C. perfringens degrade LAHPO and C. ramosum degrade LA, which was consistent with the resistance of the corresponding species to the fatty acids. A similar trend in the resistance to and degradation of the fatty acids was found with B. adolescentis and B. infantis. Much higher degradation abilities were observed in the live bacterial cells than the heat-killed cells of B. adolescentis, C. perfringens, and E. coli, suggesting that they can enzymatically degrade LAHPO in vitro.