Probiotics are live micro-organisms administered to provide health benefits. Probiotics are being increasingly used in healthcare contexts both in research studies and routine practice, for example in neonatal intensive care. Currently there is a paucity of guidelines or regulations governing the mitigation of infection risks associated with the use of probiotics in clinical practice. We propose a number of recommendations to mitigate risks. These include the communication of probiotic use to appropriate stakeholders, ensuring that routine laboratories can identify and test the susceptibility of probiotic strains, assuring standards for preparation and administration, and ensuring surveillance designed to capture adverse events.