Despite advances in prophylaxis and therapy, infections remain a major source of morbidity and mortality after lung transplantation. Lung transplant recipients are at increased risk for both community-acquired and nosocomial pathogens, which may develop at various time points. The risk of infections increases with the intensity of immunosuppression. Careful assessment of the recipient is essential to assure adequate prophylactic or preemptive therapy. Aggressive prophylaxis for some infections (e.g., cytomegalovirus) has substantially reduced the prevalence of serious infections due to this organism. Tuberculin-positive individuals should be treated with prophylactic isoniazid to reduce the chance for reactivation of tuberculosis following transplantation. Myriad opportunistic pathogens (including various viruses, bacteria, fungi, etc.) may complicate transplantation, owing to the effects of multiagent immunosuppressive therapy. This review addresses the salient pathogens that may infect organ transplant recipients, and discusses strategies to prevent or treat specific pathogens in this highly susceptible patient population.