The fungal communities inhabiting apartments in multifamily buildings ( N = 33 apartments) with natural ventilation were determined during seasonal variation in the south part of Poland (Silesia region). It was found that the average level of CO2 concentration usually not exceeded 1000 ppm. The minimal value was noted in November – 402 ppm, however the maximal concentration was equal 6156 ppm and obtained in June. The average fungal colony forming units (CFU/m3) was calculated as follows: 1.06 × 102 (February), 1.17 × 102 (June) and 2.98 × 102 (November). The most frequently occurred species/genera: yeast and yeast-like fungi, Aspergillus niger, Penicillium spp., Cladosporium cladosporioides, Rhodotorula rubra; Culvaraia lunata, Dematiaceae family, Ulocladium consortiale, Verticillium spp.; Fusarium spp., Alternaria alternata; Oidiodendron griseum. The cluster analysis showed no mutual similarity between communities of air fungi isolated from bathrooms of all studied apartments as well as between communities isolated from other indoor spaces (rooms, kitchens, halls). This suggests that natural ventilation has no (or minimal effect) on the propagation of fungal spores between apartments. Statistically significant positive correlation between the concentration of fungi in the air and external humidity, carbon dioxide levels (February, November), and external temperature (November) were found. This study provides that natural ventilation has no effect on the spread of fungal spores inside the building and are not contributed to increase of fungal airborne health risk transmission. It also shows evidence of seasonal changes in carbon dioxide in multi-family homes with natural ventilation. This may give input to establish CO2 benchmark data in such type of buildings.