The gastrointestinal tract (GIT) microbiota plays an important role in host health due to its involvement in nutritional, immunologic and physiological functions. Microbial imbalances have been associated with enhanced risk of specific diseases. This observation has allowed the introduction of microorganisms as probiotics which are microbes with demonstrated health benefits in humans when ingested in foods. The mechanisms of action include the inhibition of pathogen growth by competition for nutritional sources and adhesion sites, secretion of antimicrobial substances, toxin inactivation. Consequently, the primary clinical interest in the application of probiotics has been in the prevention and treatment of gastrointestinal infections and antibiotic-associated diarrhea diseases. The well-characterized immunomodulatory potential of specific probiotic strains, beyond the effect on the composition of the microbiota, has been be used as innovative tools to alleviate intestinal inflammation, normalize gut mucosal dysfunction, and down-regulate hypersensitivity reactions. Clinical efficacy of specific probiotic strains has been demonstrated in, rotaviruss diarrhea, antibiotic associated diarrhea, irritable bowel syndrome and food allergies. Further, recent clinical and nutritional studies have uncovered the function of specific strains in energy metabolism and thereby have opened up new angles on their exploitation. However, as these processes are highly specific, it is important to characterize the properties of specific probiotic strains an in order to select the best strains or strain combinations for the target in question. Advances have prompted increased the interest of researchers and industry and new applications and targets are being discovered.