The indoor air environment can potentially place patients at greater risk than the outside environment because enclosed spaces can confine aerosols and allow them to build up to infectious levels .It becomes imperative to undertake a study of the microbiological air quality of the airborne micro-flora in the environments of two major hospitals, Ruby Hall Clinic and Jehangir in Pune- India. In Jehangir hospital Staphylococcus aureus (15.74%) was found to be the most common organism. The correlation between the location of sampling and concentration of Staphylococcus aureus showed patient room (65±3)> neonatal ward (22±1.41)> intensive care unit (22±2.82)> operating room (16±1.73)> the main entrance of the hospital (0±0).  While Staphylococcus aureus (25.2%), followed by coagulase negative Staphylococcus (21.78%) and M. luteus (16.28%) were found to be the most common in a Ruby Hall hospital. The correlation between the location of sampling and concentration of Staphylococcus aureus in Ruby hall hospital , showed patient room (45±4.24)> intensive care unit (22±2.82)> neonatal ward (12± 2.80)> operating room (8±1.41)> the main entrance of the hospital (3±2.85). Aspergillus spp., Penicillium spp., Rhizopus spp. and Alternaria spp. were isolated in both hospitals. Maximum bacterial rates were detected in the patient rooms, while minimum bacterial rates were detected in the operating rooms and neonatal wards. The time of visit showed higher microbial rates in hospital.