In this era of immunosuppression and transplantation, it is imperative that laboratory scientists remain in close communication with physicians. In patients receiving immunosuppressive therapy, the diagnosis of mycoses must be rapid, which is complicated, requiring the cooperation and collaboration of a number of professionals from various fields of expertise. In this paper, the laboratory diagnosis of pulmonary fungal infection is reviewed. The following topics are included: host factors such as immunological response and predisposing anatomical features; collection, transport and storage of specimens; laboratory processing of samples; direct microscopy; staining techniques, culture and identification of fungi; laboratory biosafety; tissue tropism and reactions; serology; and antigen detection.