This study aims to evaluate the correlation between fungi causing paint deterioration and air contamination in Assiut University hospital to give a complete picture for the fungal quantity and spectrum. Seventeen fungal species were isolated from 15 samples of deteriorated water-based paint collected from the hospitals. Chaetomium globosum was the most common paint-deteriorating fungal species, followed by Alternaria alternata, Aspergillus parasiticus, Penicillium oxalicum and Setosphaeria rostrata. Direct examination confirmed the ability of these fungi to colonize the paint samples producing mycelia, conidia and fruiting bodies. In vitro, these fungi exhibited high potential to utilize the thin layer of polyacrylic paint and significant enzymatic activities of cellulase, lipase and urease that may play a main role in paint degradation and as virulence factor of human diseases. Moreover, 27 fungal species were isolated as air contaminating mycobiota. Aspergillus spp., Cladosporium cladosporioides, P. oxalicum, A. alternata and C. globosum caused a considerable amount of indoor air contamination. The results indicated that there is a clear correlation between fungi causing paint deterioration and air contamination, whereas certain fungi were responsible for wall paint deterioration and frequently indoor air contamination. The current study suggests that improvement of antimicrobial additives of paints may be a promising approach to reduce paint biodeterioration and subsequently air contamination of indoor environments.