The human intestine is colonized by a large number of microorganisms, collectively termed microbiota, which support a variety of physiological functions. As the major part of the microbiota has not yet been cultured, molecular methods are required to determine microbial composition and the impact of specific dietary components including probiotics. Probiotics are viable microbial food supplements, which have a beneficial impact on human health. Health-promoting properties have been demonstrated for specific probiotic products. The most significant demonstrations for probiotic efficacy include prevention and treatment of antibiotic associated diarrhea, rotavirus diarrhea and allergy prevention. Lactobacillus rhamnosus GG (=ATCC 53103) and Bifidobacterium lactis Bb12 are the among the best-characterized and most studied probiotic strains with demonstrated impact on human health. New complex targets for probiotics include irritable bowel syndrome and Helicobacter pylori infection. For future probiotics the most important target is a demonstrated clinical benefit supported by knowledge on the mechanistic actions in the microbiota of the target population. Molecular and genomics-based knowledge of the composition and functions of the microbiota, as well as deviations from the balanced microbiota, will advance the selection of new and specific probiotics. Potential combinations of specific probiotics may prove to be the next step to reduce the risk on intestinal diseases and reconstruct specific microbial deviations.