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There is increasing scientific evidence of the adverse health effects of indoor exposure to a collective mixture of chemicals in children. People spend 80–90% of their time indoors, breathing air that is often even more polluted than the air outside. This study presents results of school inspection and sampling of selected chemical pollutants—formaldehyde, benzene, and nitrogen dioxide—in classrooms and outdoors in ten schools in Kosovo, conducted by the National Institute of Public Health and the WHO. Nitrogen dioxide and benzene were most affected by outdoor concentrations and were too high in at least one school (NO2: >80 µg/m3, benzene: 1–2 µg/m3). Formaldehyde was significantly higher indoors than outdoors and higher in newer schools than older ones, but overall levels were not alarming (maximum around 20 µg/m3). CO2 levels during class indicated insufficient ventilation. The temperatures were occasionally too high during the cold season. This not only results in unnecessary energy wastage but also too low relative humidity. Improvements in air circulation and temperature control, as well as the identification and elimination of certain sources of pollution would improve the health and learning of school children.