Recognition of and therapy for fungal infections of the lungs still presents problems even for the experienced clinician. The distinction between invasive mycoses of the lungs and fungal colonisations that do not require therapy is cinically difficult and can often not be made satisfactorily even with advanced microbiological diagnostics. One must differentiate between a primary, often locally limited, endemic pulmonary mycosis and a pulmonary mycosis against the background of a locally or systemically compromised immune system. Patients at risk include those with advanced HIV infections, patients under long-term antibiotic therapy as well as oncological and multimorbid patients. The pulmonary manifestation of a mycosis may not only be the starting point for a systemic dissemination but can also arise in the course of hematogenous spread of the infection. The latter can appear, for example, as an invasive pulmonary aspergillosis in immunesuppressed patients. Thus, early clinical, radiological and biological confirmation of the diagnosis is essential in order to avoid the possible complications of pulmonary mycosis.