Surgical consultation is regularly requested for diagnosis and treatment of pulmonary complications of the endemic mycosis, Histoplasma capsulatum, Blastomyces dermatitidis and Coccidioidomycosis immitis, and the yeast Cryptococcus neoformans. All resemble pulmonary malignancies. Histoplasmosis causes pericarditis, mediastinal fibrosis and mediastinal granuloma, which can cause entrapment of vascular structures, the esophagus, and the trachea. Coccidioidomycosis can cause spontaneous pneumothorax and thin wall cavities that can be superinfected with tuberculosis and Aspergillosis. The pathogenesis, diagnosis, and treatment of these organisms are discussed with emphasis on the new oral therapies and complications encountered in persons with human immunodeficiency virus (HIV) infection.