The aim of this study was to test the air in a single hospital department for fungal contamination. The department included three fully protected rooms with laminar air flow, comprising a bone marrow transplant unit (BMTU) and eleven naturally ventilated patient rooms of a haematology unit (HAEMU). Air samples were taken with an IDEAL air sampler (bioMerieux) on Sabouraud dextrose agar plates. The concentration of fungi in the air of the HEPA-filtered rooms of the BMTU ranged from 0-75 CFU/m³. Penicillium and Cladosporium were dominant among the fungal biota in the whole department. Of aspergilli, A. fumigatus was prevalent and seasonal increases in the frequencies of A. clavatus and A. niger isolation were observed. The detection of potentially pathogenic species of Aspergillus and Mucor in the BMTU and an increased concentration of Aspergillus in the HAEMU (up to 200 CFU/m³) instigated the introduction of additional preventive measure besides routine disinfection, namely an exchange of the HEPA filters in the BMTU and the installation of equipment based on multifunctional ion technology in the HAEMU. In a subsequent examination, a diminished number of fungi in the air was observed. During the study, 2 cases of proven and 3 of probable aspergillosis (according to EORT criteria) were noted. There was no link observed between the higher concentration of Aspergillus detected in the hospital air and the development of the infection. The authors conclude that hospital air examination can be helpful in indicating problems with hospital air facilities, enabling the introduction of procedures improving air quality and subsequently diminishing the risk of nosocomial mycoses.