ObjectiveTo explore the value of bronchoscopy alveolar lavage cytology in diagnosis of pulmonary fungus infection and distinguishing colonization from true fungal infections. MethodsA retrospective analysis was conducted on the patients with positive fungi results in bronchoalveolar lavage cytology admitted in Shanghai Xinhua Hospital between January 2009 and December 2013.Clinical,radiological,bronchoalveolar lavage and histopathology findings were recorded and analyzed. ResultsFungi were found in alveolar lavage fluid in 60 cases.The most common fungal organism identified was Aspergillus,followed by Candida and Cryptococcosis.Twenty-seven cases (45.00%) by lung biopsy pathology were diagnosed as pulmonary fungal infection and 33 cases (55.00%) were diagnosed as lung bacteria colonization.Aspergillus was found in 35 cases (58.33%),as pathogenic bacteria in 12 cases (34.28%),and colonization bacteria in 23 cases (65.72%).Candida was found in 13 cases (21.67%),as pathogenic bacteria in 3 cases (23.08%),and colonization bacteria in 10 cases (76.92%).Ten cases of Cryptococcus and 2 cases of pulmonary sporozoan were all as pathogenic bacteria.Most cases of Aspergillus and Candida in cytological specimens presented as a pulmonary mass or endobrochial growth and were diagnosed as carcinomas in biopsy specimens,so bacteria colonization should be considered in these cases first of all.All cases of Pneumocystis with bilateral ground glass infiltrates and cryptococcosis with parenchymal mass lesion in radiology represented true infection.The coincidence rate of bronchoscopy alveolar lavage cytology and histopathology was 45%. ConclusionAspergillus and Candida species are the most common fungal organisms in the bronchoscopy alveolar lavage.Fluid cytological examination is an important diagnostic modality for pulmonary mycoses,however it is important to correlate with clinical,bronchoscopy and biopsy findings for accurate diagnosis and appropriate management.