Many trials on probiotics are now published that use established methods to demonstrate their clinical efficacy. Convincing progress has been made in the field of inflammatory bowel disease and allergy prevention in infants. Experimental studies show clear differences (and even sometimes opposite effects) between apparently closely related probiotics and suggest new mechanisms for the observed effects, such as immunostimulation by bacterial DNA and interaction with Toll-like receptors and dendritic cells in the gastrointestinal tract.