Hospitalized patients have a potential risk for nosocomial infections. Airborne fungi are one of the main causes of fungal infections in this group. The objective of this study was to investigate the concentrations and species of airborne fungi in two general hospitals in Shiraz, southern Iran. Air samples were collected from high-risk wards, using settle plate method. Fungal colonies were identified, enumerated, and reported. A total of 1075 microbial colonies were detected, 419 of which were fungi. Fungal isolates from two hospitals, belonged to 15 genera. 4.25% of rooms in hospital A and 16% in hospital B were clean rooms. Cladosporium followed by Aspergillus spp were the predominant genus in two hospitals studied. The highest fungal deposition rates were 1016 and 1797 CFU/m2 in Emergency and Surgery rooms. Monitoring airborne fungi is one of the best ways for prevention and control of these infections. Caring for high-risk patients in hospital rooms has lead to reduced rates of nosocomial fungal infections.