Probiotics discussed in this paper are evaluated using the WHO/FAO definition from 2001. The authors present a brief description of the normal microbiota of the gastrointestinal tract, discuss probiotics in the aspects of gut immunity and then move to selection of bacterial strains as probiotics. The main issue raised is the critical evaluation of probiotics in randomized clinical trials for conditions such as: infectious diarrhoea; antibiotic associated diarrhoea; inflammatory bowel disease; pouchitis and diverticulitis; H. pylori infection; irritable bowel syndrome. Safety of probiotics is mentioned with respect to susceptible individuals and bacterial translocation. As a conclusion the authors again recall the strain specific actions of probiotics in different clinical situations and that so far probiotics play a role in rotaviral and post antibiotic diarrhoea and pouchitis. An important issue still to be solved in order to confidently recommend probiotics as efficacious therapy is the regulatory aspect of probiotics.