Probiotics are live, microbial food supplements that benefit the host animal by improving intestinal microbial balance. Their major role in preventing and treating gastrointestinal disease appears to be from their effect on the immune process, protection against abnormal invasive bacteria, and in the production of short-chain fatty acids from starch and non-starch polysaccharides. Probiotic microorganisms are administered in food supplements and yogurts. They are also now sold in the form of capsules and powders. There is great variation in the microorganisms in the various supplements. It is important to understand that all probiotic products are different. Some contain a single organism and others contain multiple organisms. Therapeutic results have been achieved with various probiotics in different diseases. In the treatment of inflammatory bowel diseases (IBD), success has been reported with Escherichia coli Nissle strain in ulcerative colitis, and with a multiple organism product, VSL#3 (VSL Pharmaceuticals, Fort Lauderdale, FL), in Crohn’s disease and pouchitis. Initial reports in irritable bowel syndrome (IBS) have resulted in encouraging results with the use of E. coli Nissle strain, and recently with multiple organism probiotic supplements. However, caution must still apply to the use of probiotics in IBD and IBS because the reports and the number of patients treated are limited.