Quercetin, a naturalflavonoid has high potential for management of inflammatory bowel diseases (IBD).However, its onset of action is delayed when administered systemically and high doses are needed for IBDtreatment. The present study aimed to develop chitosan microparticles for colonic delivery of clinically relevantquercetin concentrations as a potential treatment for IBD. Different formulations of quercetin microparticleswere prepared and evaluated in terms of pharmaceutical, morphological and compatibility aspects. Thein vitrorelease profiles of acid-resistant capsulesfilled with quercetin microparticles showed that most of quercetin wasreleased in IBD colon simulating medium. Rabbit colitis model was used to evaluate the therapeutic effects ofquercetin microparticles based on various assessment criteria (e.g.index of tissue edema, clinical activity score,colon macroscopic and histopathological characteristics, biochemical assays of the levels of myeloperoxidaseenzyme and tumor necrosis factor-αand the activities of superoxide dismutase and catalase). The animalstreated with quercetin microparticles had significantly improved therapeutic outcomes as compared to thosetreated with plain drug and the untreated animal controls. The results demonstrate that the developed quercetinmicroparticles have suitable pharmaceutical properties and mightfind clinical applications in acute IBD man-agement.