The potential ‘nutritional advantages’ of probiotics and prebiotics consist of preventive, and sometimes curative, effects against certain diseases. The evidence supporting such advantages, which requires randomised controlled trials and consistency of results from study to study, is rapidly increasing. This article summarizes the effects against diseases of intestinal origin. There is a high level of evidence for positive effects of some prebiotics to alleviate constipation and treat hepatic encephalopathy. Interesting aspects, but with a lower level of evidence at the present time, include prevention of colon cancer, intestinal infection, and recurrence of inflammatory bowel disease. There is a high level of evidence for positive effects of some probiotics in the alleviation of lactose intolerance, antibiotic-associated intestinal disorders and gastroenteritis. Evidence is rapidly growing regarding the prevention of recurrence of inflammatory bowel diseases. Positive trials have suggested preventive effects against intestinal colonization with specific gut pathogens including Clostridium difficile and Helicobacter pylori.