The interactions of the gastrointestinal microflora with human health has been the subject of considerable debate in recent years. Disruption of the ecologic equilibrium of the normal intestinal flora may result in gastrointestinal diseases such as rotavirus diarrhea, antibiotic associated diarrhea, traveller's diarrhea and colon cancer. Functional foods, which are used in prevention and treatment of some intestinal diseases, are defined as “foods that may provide health benefits beyond basic nutrition”. Probiotics are constituted an important part of functional foods. Probiotics are live microbial food supplements that beneficially affect the host by improving its intestinal microbial balance. Some of the claims for which research supports a benefical effect of probiotic consumption include: improving intestinal tract health, enhancing the immune system, reducing symptoms of lactose intolerance and costipation, and reducting risk of certain cancers. This article discusses the impact of probiotic bacteria on different gastrointestinal diseases from a wide perspective by using new literature data.