Probiotics are microorganisms which, when ingested, may have a positive effect in the prevention or treatment of a specific pathologic condition. Probiotics are used for a number of gastrointestinal and certain systemic infectious and inflammatory diseases. The efficacy of selected probiotics to promote recovery from acute viral gastroenteritis in young children is well-documented. However, the role of probiotics in systemic diseases, e.g. atopic dermatitis, need to be confirmed in larger randomised controlled trials. This paper describes the theoretical background for the use of probiotics and reviews results from randomised controlled trials describing the effect of probiotics, particularly in paediatric diseases.