Air harbors a substantial number of microorganisms the assessment of which is critical for healthy human living. The assessment of airborne bacteria and fungi in and around three hospitals in southwest Nigeria; the University Teaching hospital Ibadan, Oyo state, the State hospital Ota, Ogun state and a private hospital in Lagos state were carried out using the open petri dish sedimentation technique for three months between March and May 2014 at two weeks intervals. The survey yielded numerous and diverse assemblages of bacteria and fungi. Nineteen bacterial species belonging to twelve genera were isolated namely Alpha-haemolytic Streptococcus, Staphylococcus aureus, S. epidermidis, Escherichia coli, Enterobacter sp., Micrococcus luteus, M. varians, Corynebacterium xerosis, C. kutsceri, Lactobacillus fermentum, L. casei, L. delbruekii, Pseudomonas aureginosa, Clostridium sp., Enterobacter sp., Proteus sp., Streptococcus sp., Klebsiella sp., and Mycobacterium sp. The fungal assemblages were composed of Aspergillus fumigatus, A. flavus, A. niger, Arthrobotrys sp., Alternaria sp., Bipolaris spicifera, Curvularia clavata, C. affinis, Chrysosporium corda, Candida albicans, Cladosporium sp., Cryptococcus sp., Diplodia sp., Esepedonium sp., Fusarium sp., Geotrichum sp., Humicola sp., Monilia sp., Mucor sp., Penicillium sp., Rhizopus nigricans, R. stolonifer, Talaromyces sp., Torula nigra, and Trichoderma sp. Among these are pathogenic species to which both patients and visitors get exposed to while visiting the hospitals, thereby coming down with nosocomial infections. Some end up worse than they were, while healthy ones get infected coming down with different diseases. The overall assessment highlighted the sanitary conditions of the different units in the hospitals and the need for more aggressive sanitation measures.