This opinion statement discusses indications, efficacy and safety of probiotics in immunosuppressed patients. The best evidence available is for the prophylaxis of infections in patients after liver transplantation and for patients with liver cirrhosis. For other organ transplantations and for bone marrow transplantation the efficacy of probiotic interventions has not been proven yet, but in these patient groups safety is a concern. Also in critically ill patients, the data on efficacy are inconclusive and safety is a concern. In HIV patients and patients after major surgery, probiotic bacteria seem to be safe since there are no associations with increased risks of side effects.