Aims: The aim of this study was to evaluate the bioaerosols level in the various parts of three educational hospitals of Isfahan, Iran. Materials and Methods: The collection of bioaerosols (including bacterial and fungal microorganisms) was carried out with one-stage Anderson sampler. The sampling was carried out at the height of 1.5 m from the floor of various hospitals wards (infectious, surgery, urology wards, and operating room). The volume of each sample was determined based on pre-tests carried and was about 50 L. After sampling, the samples were incubated and analyzed. The effect of various environmental conditions including humidity, temperature, and outdoor bioaerosol levels was also investigated. Results: The lowest numbers of fungal and bacterial concentration were obtained in operating rooms of the hospitals and the highest concentration was observed in infectious disease wards of hospital 1 and 2 and surgery ward of hospital 3. The bacterial concentration was observed to be higher in hospital wards than outdoor, except hospitals' operating rooms. Conclusion: The findings showed that the bioaerosols level in the hospitals was relatively high. The higher levels of indoor bacteria than outdoor might be associated with the presence of patients, their activity, unsuitable ventilation, and disinfection. Therefore, environmental monitoring and control measures are required to improve hospital environmental quality especially in the wards with immune deficiency patients.