BACKGROUND: Emphasis has been placed on the need for antifungal prophylaxis when transplanted organs are directly exposed to the environment. In lung transplantation, one strategy for prevention has been aerosolization of polyenes into the lung. Despite widespread use of amphotericin B aerosols, there are still few studies on how to validate their effectiveness or optimize pharmacokinetics. METHODS: We compared results of several of our own studies of lung transplant recipients receiving formulations of amphotericin B with results of other studies. RESULTS: Recent aerosol studies suggest that aerosols of a lipid formulation of amphotericin B are safe and better tolerated than is amphotericin B deoxycholate. Their use in prophylaxis is associated with very few pulmonary fungal infections. CONCLUSION: This safe drug delivery at a local body site to directly protect the transplanted organ without systemic antifungal drug exposure is attractive from a cost and toxicity standpoint. However, careful multicenter, comparative studies are still needed to ensure that this strategy is consistently successful.