Fungi are ubiquitous and the respiratory tract is exposed to aerosolized spores of both fungi that are “pathogenic” even in the normal host, such asCryptococus neoformans, and those that are “opportunistic”, such asCandidaandAspergillusspecies, among others. Although these latter species may occasionally form fungal balls or induce allergic phenomena in the normal host, they produce more invasive diseases in immunosuppressed patients. Among these diseases, pseudomembranous aspergillosis has recently been described.The diagnostic approach to these entities, and, in particular, the thin dividing line between colonization and infection are addressed, along with the diagnostic value of the various procedures.New prophylactic regimens are reviewed such as the possibility of using amphotericin aerosols in combination with systemic azole administration.The authors would emphasize the importance of restoring lung defences by not only decreasing immunosuppressive regimens but also considering the use of newly available recombinant cytokines such as growth factors, to reduce neutropenia, for instance, in addition to antifungal drugs when infection is diagnosed. However, immunomodulation procedures are far from being well established.