Air sampling was done inside adult and children's hospitals that were selected to treat severe cases of COVID-19. Influence of peripheral factors such as particle concentration, air velocity, sampling point dimensions, distance from the patient bed, sampling time, the flow rate of sampling pump, and factors related to COVID-19 patients (disease period, mask use, number, and age) were analyzed using multivariate analysis (RT-PCR). The results showed that 5.8% (N = 8) of indoor air samples were positive for the presence of the coronavirus. The presence of viruses in the indoor air of hospitals has a strong positive relationship with particles and the age of patients while it has a reverse relationship with the air cleaner, ventilation system, and distance from the patients. Therefore, the higher particle concentration, the age of hospitalized patients, and the remarkable number of patients increase the probability of the presence and identification of the coronavirus in the indoor air of hospital wards. Also, the presence of an air cleaner, a suitable ventilation system especially a mechanical one, and increasing the distance from the patients reduces the possibility of virus existence in the indoor air and its identification. In general, the results showed that the adult hospital has more polluted indoor air than the children's hospital in terms of the presence of SARS-COV-2. Sanitation and engineering measures like upgrading the ventilation system, particularly in vulnerable wards of hospitals are recommended.