Although a biopsy may need to be performed in complicated patients, bronchoalveolar lavage (BAL) is an important adjunct to the diagnosis of pulmonary and disseminated fungal infections. Culture is the gold standard for diagnosis in many instances, but cytologic and morphologic analysis is often diagnostic. Although newer molecular and antigen techniques may be applied to BAL samples, the role of such tests is yet to be defined for many pathogens.