Dysbiosis is a prominent feature of inflammatory bowel diseases (IBD). However, the efficacy of using antibiotics aiming at the aberrant gut microflora for IBD treatment are either unsuccessful or not persistent. In contrast, long-term oral vancomycin has been proved effective in controlling both the bile duct and gut inflammation of primary sclerosing cholangitis (PSC), an autoimmune disease against the intra- and extrahepatic bile ducts that holds a high rate of concomitant IBD and shares many common characteristics with IBD, including similar dysbiosis patterns. Two discrepancies of antibiotic usage might explain the dramatically different responses of the two diseases toward this strategy. First, the vast majority of antibiotic formulas for IBD management consist of broad-spectrum antibiotics mainly targeting gram-negative bacteria with some covering anaerobes and gram-positive ones, while vancomycin used for PSC treatment almost exclusively targets gram-positive bacteria. Several lines of clues suggested that gram-positive microorganisms might be responsible for the chronic inflammation observed in IBD and PSC. Second, improvement of liver test in PSC patients is usually observed after a relatively long period of oral vancomycin treatment (more than 12 weeks) and it takes even longer for gut mucosal healing. Moreover, long-term low dose oral vancomycin is required to prevent PSC recurrence. However, most trials of using antibiotics for IBD management is aiming at inducing remission with short treatment course (most less than 2 weeks) without maintenance. We hypothesize that the host antimicrobial response favors the growth of certain gram-positive intestinal bacteria in genetically predisposed individuals which is responsible for the aberrant immunological reaction towards the gut mucosa. Oral vancomycin induces disease remission by suppressing the pathogenic gram-positive microorganisms, but long course is needed since the gut inflammation is usually severe than that concomitant with PSC. Moreover, long-term maintenance is required to prevent the rebound of the pathogens and flare of the intestinal inflammation.