The pathogenesis of inflammatory bowel diseases remains elusive. However, the resident luminal bacteria seem to be an important factor in their development and chronicity. There is evidence to suggest that inflammatory bowel diseases may represent an aggressive immunological response to the resident luminal flora, rather than an alteration in the normal flora. In prior research, probiotic bacteria were effective in managing certain acute diarrheal diseases, and investigators reported that certain Lactobacilli strains seem to have protective immunomodulating and bowel flora manipulating properties. We report the results of recent studies with probiotics in animal models, in which promising effects for the treatment of chronic inflammatory bowel disease, pouchitis, and ulcerative colitis were observed. Future research may clarify a precise role for probiotic bacteria in managing chronic inflammatory bowel diseases.