Probiotics are live microbial feed supplement which beneficially affects the host animals by improving its microbial balance. Probiotics have been used in the treatment of bacterial or viral induced acute intestinal infection. In recent years, some clinical studies have shown the therapeutic effects of probiotics in the treatment of chronic inflammatory bowel disease (IBD) or prevention of allergic disease. Evidence exists for therapeutic use of probiotics in acute infectious diarrhea, Clostridium difficile colitis and antibiotic-associated diarrhea. Their exact role in IBD, irritable bowel syndrome and prevention of cancer has not to be determined. This review summarized the data about probiotics in gastrointestinal diseases and examine the mechanisms of action related to their therapeutic effects.