Advances in the therapy of tumors or for the maintenance of grafts have improved survival in a large number of patients, but at the price of repeated complications due to the induced immunodeficiency state. Pulmonary infections are a frequent occurrence, and while some are easily recognized and treated, others must be precisely diagnosed, as only early specific treatment can avoid the often fatal outcome. Various techniques have therefore been developed to obtain specimens for microorganism isolation before having ultimate recourse to a surgical lung biopsy. It is in this field that the most marked progress is currently being made. The different microorganisms responsible for these affections are reviewed, the majority being common to the immunodeficiency state, while others are encountered more frequently as a function of the underlying disorder and of the ecological conditions in each centre.