Infection is a frequent complication of organ transplantation and is associated with significant morbidity and mortality. Preventative antimicrobial strategies are a key component of the care received by transplant patients. This review summarizes the evidence supporting anti-infective prophylaxis in this setting. Specific recommendations for the prevention of bacterial, fungal, viral and parasitic infection after transplant are made, with a focus on recent developments in the field of transplant infectious diseases.