Oral administration of a probiotic preparation was shown to be effective in preventing the recurrence of chronic pouchitis in a classic double‐blind, placebo‐controlled trial. This was a novel and unique approach to the care of these patients. Dysbiosis, a condition of microbial imbalance, has been implicated in the pathogenesis of inflammatory bowel disease. Rather than administering antibiotics to treat the microflora with each relapse of pouchitis, the emphasis was placed on preventing chronic flare‐ups by administering probiotics to correct dysbiosis. The paradigm was shifted from treatment to prevention and from antibiotics to probiotics. These data were validated by this same group and others in subsequent trials. However, despite the promising results, many questions will need to be answered before routine use becomes universally accepted. The exact etiology and pathophysiology of pouchitis have not been fully elucidated. In addition, the choice of bacteria, optimal dose, and timing of administration have yet to be determined. Finally, the mechanisms by which probiotics provide their beneficial effects remain unresolved.