Most nosocomial pathogens cause pneumonia through the following sequence: transit to the patient on the hands of medical personnel or perhaps in food, proliferation in the nasopharynx, and subsequent pulmonary aspiration. There are three exceptional pathogens, each of particular concern as a cause of pneumonia in the immunocompromised patient, which follow atypical routes. Important recent advances in understanding these routes permit more rational preventive measures. This report examines the evidentiary basis for the following pathophysiolgic propositions about these three pathogens: Aspergillus, Pneumocystis carinii, and Legionella. Aspergillus spores are almost ubiquitous. Spore generation, except in very unusual circumstances, takes place outside the hospital. Most spores enter the hospital borne in air by infiltration or because of incomplete filtration. Air filtration systems of moderate efficiency remove Aspergillus spores. Nosocomial pulmonary and disseminated aspergillosis arises from inhalation of airborne spores. A nasopharygeal colonization intermediate step before pulmonary disease has not yet been solidly established. It is now firmly established that airborne Pneumocystic carinii transmission occurs between animals. Airborne acquisition probably occurs early in human life. However, in-hospital, person-to-person transmission has yet to be convincingly demonstrated. Most or all cases of pneumocystosis in adults are due to reactivation of endogenous pulmonary organisms. Intensive diagnostic efforts reveal that Legionella is a common cause of community-acquired and nosocomial pneumonia in hospitals where it had not previously been recognized. However, there are at least a few hospitals where it is an uncommon source of pneumonia. Several hospitals have demonstrated a temporal association between the presence of Legionella in hot water systems and nosocomial cases of Legionella pneumonia. The mechanism or mechanisms of transmission to the patient remain to be delineated. It is also not determined if all hospital hot water systems should be maintained Legionella free.