Insight into the diversity and function of the human intestinal microbiota has been stimulated by clinical studies with bacteria that exhibit specific functions and which are marketed as probiotics to positively affect our health. Initial efforts concentrated on establishing sound scientific support for the efficacy of these probiotic bacteria, which mainly include Lactobacillus and Bifidobacterium species. Following these evidence-based functional approaches, considerable research is now focused on the mechanisms of action of probiotic bacteria. The mechanisms identified to date mainly relate to the stimulation of host defence systems, immune modulation and the competitive exclusion of pathogens. Recent efficacy, molecular and genomics-based studies have also been reported for some probiotic strains that have found their position in the market place.