Background: The frequency of fungal infections of the lung has increased particularly in immunocompromised patients. Early diagnosis and treatment is important to start antifungal therapy and to avoid unnecessary use of toxic antifungal agents. This study aimed to identify the common fungal species causing pulmonary infection in immunocompromised patients and their in vitro antifungal sensitivity pattern in Assiut University Hospitals (AUH). Subjects and Methods:This was a hospital based descriptive study conducted on 135 patients admitted at different Intensive Care Units (ICUs) and Oncology Department at Assiut University Hospitals (AUH). Collected respiratory specimens were subjected to direct microscopic examination and inoculation on Sabouraud Dextrose Agar (SDA). Identification of isolated yeasts was done using phenotypic methods including chromogenic media (Brilliance Candida agar and CHROMagar Candida differential media), germ tube test, cornmeal agar and API candida while mould isolates identification was mainly dependent on macroscopic and microscopic features. Some isolates had confirmed using rRNA gene sequencing. In vitro antifungal susceptibility testing was done using disc diffusion method.Results: In this study 80/135 (59.3%) of collected samples were positive for fungal infection. The most common fungal pathogens isolated were Candida and Aspergillus species. In vitro sensitivity test showed that the yeast isolates had the highest sensitivity to Nystatin (90.9%) followed by Amphotericin B (80.3%) while for mould isolates, the highest sensitivity was to Voriconazole (71.4%) followed by Amphotericin B (57.1%). Conclusion:Pulmonary fungal infection appears to be an important problem in immunocomprimised patients with Candida albicans was the most commonly isolated yeast from various clinical specimens; also the increase in the resistance especially to azoles is a major concern.