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The significance and clinical management of Candida colonization of the respiratory tract are ill-defined. We now report the frequency of Candida species from the lower respiratory tract in hematopoietic stem cell transplant recipients (HSCT) undergoing bronchoscopy with broncheoalveolar lavage for pneumonitis after HSCT. The University of Michigan Clinical Microbiology Laboratory Database was queried for all respiratory cultures positive for Candida species between 2000 and 2012. We concurrently performed a retrospective analysis of 515 HSCT recipients with pneumonitis at our institution between 2001 and 2012. During this 12-year period, there were 2524 unique Candida isolates (78% Candida albicans). Of the 515 HSCT patients with suspected pneumonitis, 127 (24.7%) HSCT subjects were culture positive for a fungal pathogen, with Candida species identified in 27 cases (5.2%). When compared with other HSCT subjects, those cultures positive for Candida had significantly increased mortality (P=0.04). Candida sp. are commonly cultured from the respiratory tract of HSCT recipients, with increased mortality in affected patients. While there is insufficient evidence for antifungal treatment of Candida species colonization, the presence of the yeast may be useful as a surrogate marker of disease severity.