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A healthy indoor environment is becoming an increasingly important issue. As the use of various materials in inhabited interiors increases, so does the concentration of harmful volatile organic compounds (VOCs) in these spaces. The actual trend of reducing energy consumption in buildings, such as by using perfectly sealing windows and doors, contributes to this increase. Consequently, people moving around in these interiors experience a rise in health problems due to the elevated concentrations of VOCs. This study aimed to assess the indoor air quality (IAQ) in naturally ventilated primary schools located in the southern Czech region. Two classrooms were selected from each primary school based on similar characteristics, such as building construction, volume, windows structure, area of windows, number of occupants, activities, type of furniture, and internal covering including flooring, wall, and ceiling. The classrooms were continuously occupied during school hours for a total of 25-35 hours per week and unoccupied during afternoons and weekends. The study focused on measuring the concentrations of volatile organic compounds (VOCs) in the classrooms, as well as assessing their impact on health. The study highlights the importance of monitoring IAQ in naturally ventilated primary schools and can be useful for policymakers and school administrators in developing strategies to improve IAQ and promote the health and well-being of students and staff.