The endemic mycoses are restricted geographically based on environmental and other factors that favor the growth of these organisms in the soil. Histoplasmosis and blastomycosis mostly afflict patients in the Mississippi and Ohio River Valleys whereas coccidioidomycosis occurs primarily in the dessert southwest United States. Cryptococcosis also may present as pulmonary disease, particularly in persons with cellular immune impairment. These mycoses are increasing in importance as causes for opportunistic disease in immunocompromised patients, especially those with acquired immune deficiency syndrome (AIDS). Aspergillus is a common cause of serious invasive fungal infection in granulocytopenic patients, and may cause lung infection in persons with pre-existing pulmonary diseases or atopy. Infections with less virulent fungi, such as Trichosporon, Fusarium, Alternaria, Pseudallescheria, and dematiaceous fungi, are being recognized more frequently. The lung is the portal of entry for most of these pathogens, and often is prominently involved in the clinical syndrome. This article focuses on the recognition, diagnosis, and management of these important pulmonary mycoses.