The use of probiotics, once discussed primarily in the context of alternative medicine, is now entering mainstream medicine. However, only a few of the potential health benefits attributed to probiotics have been confirmed in well-designed, well-conducted, randomized, controlled trials. This is especially true in the pediatric population. We review here the available evidence on efficacy of probiotics in children in the prevention and treatment of gastrointestinal diseases. Although we restrict our analysis to the pediatric age, whenever potentially relevant information is available only from adult studies, they are examined as well. Probiotics have been most extensively studied in the treatment of diarrheal diseases, where their efficacy can be considered well established. Studies documenting effects in other childhood gastrointestinal illnesses are few, although some preliminary results are promising. Furthermore, only a limited number of probiotic strains have been tested, and, as the effects of different probiotic microorganisms are not equivalent, results cannot be generalized. Thus, at present, we have some positive certainties, lots of exciting promises and many unanswered questions.