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The aim of the study was to compare the indoor levels of airborne bacteria and fungi of air conditioned (AC) buildings and naturally ventilated (NV) buildings using a Supermarket, a Laboratory and an Eatery as a case study. The predominant bacterial isolates were Staphylococcus, Micrococcus spp., Escherichia coli, Bacillus spp., Streptococcus spp., Enterococcus spp., Klebsiella spp. The fungal isolates belong to the genera Penicillium, Aspergillus, Mucor, Trichophyton, Fusarium, Candida and Chaetomium. The levels of airborne bacteria and fungi were determined using settle plate method. In AC buildings the average air levels of bacteria (supermarket: 24.2 CFU m-3; laboratory: 29.2 CFU m-3; eatery: 51.0 CFU m-3 air) were higher than in NV (respectively: 54.3 CFU m-3; 100.7 CFU m-3; 134.3 CFU m-3 air). The average air levels for fungal isolates were higher in the eatery due to presence of poorly maintained AC system (supermarket: 7.8 CFU m-3; laboratory: 11.5 CFU m-3; eatery: 56.7 CFU m-3 air) than in NV (28.6 CFU m-3; 19.6 CFU m-3; 13.5 CFU m-3 air respectively). Findings from this study showed that AC buildings had lower levels of bacterial and fungal contamination compared to buildings with natural ventilation.