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HVAC systems consumes 37 % of the electricity in educational buildings. Energy consumption varies depending on the ventilation strategy. School buildings have a responsibility of ensuring energy performance and maintenance of indoor environmental quality for its occupants. This study assesses the efficiency of the ventilation system in terms of the microbes present in the spaces. Microorganisms and particulate matters were sampled in classrooms, locker rooms, libraries in two high schools and an elementary school. Six bacterial species and seven fungal species were identified. The most abundant microorganisms were Staphylococcus sp., Bacillus sp., and Micrococcus sp. Elementary school, especially kindergarten, showed higher microbial concentration and particulate matter as a result of higher human activity. Microbial concentration was influenced by the types of room in the same building with the same ventilation system. Canonical correspondence plot (CCA) determined that gender and school type have significant effects. The presence of Bacillus sp., Aerococcus sp., Corynebacterium sp., and Penicillium sp. was significantly related to gender, while Staphylococcus sp. and Alternaria sp. were related to type of school. The presence of Aerococcus sp. and Micrococcus sp. depended on the distance from the vent location. Relatively lower number of Aerococcus sp. was detected when the distance between sampling site and vent was less than 2 m. Micrococcus sp. was generally detected when the distance was < 3.5 m. The distance from the door was not significant.