Pulmonary mycoses, such as invasive aspergillosis are a major threat for immunocompromised patients. Non-aspergillus mould infections of the lung are still rare but increasingly observed. Pulmonary Candida infections are also rare. Other fungal infections that can affect the lung are cryptococcosis, and endemic mycoses such as blastomycosis, histoplasmosis, coccidioidomycosis and paracoccidioidomycosis. The diagnosis of pulmonary fungal infections is difficult and may therefore frequently be delayed or even missed. Computer tomography and microbiology are the most important diagnostic approaches. Discrimination between colonization and invasive infection is a particular challenge. Antigen detection and polymerase chain reaction (PCR) are additional valuable diagnostic tools. Amphotericin B has been the drug of choice for decades. The armamentarium has been enlarged by the introduction of less toxic amphotericin B lipid formulations, of broad spectrum azoles such as voriconazole and posaconazole and of the echinocandins (caspofungin, anidulafungin and micafungin) into therapy. Voriconazole has demonstrated efficacy in the treatment of invasive aspergillosis and is now licensed for first-line treatment together with amphotericin B. Lipid formulations of amphotericin B are an option, particularly for empiric treatment. Posaconazole is also reported to be active against various emerging opportunistic moulds such as Fusarium species and Zygomycetes. Caspofungin is licensed for second-line therapy of invasive aspergillosis. Along with the antimycotic spectrum, the pharmacokinetic properties and the toxicity of antifungal drugs are crucial for therapeutic success.