BACKGROUND: The growing public health concern caused by non-communicable diseases in urban surroundings cannot be solved by health care alone; therefore a multidisciplinary approach is mandatory. This study aimed to evaluate the airborne aerosol pollution level in primary schools as possible factor influencing origin and course of the diseases in children. METHODS: Seasonal aerosol particle number concentration (PNC) and mass concentration (PMC) were studied in the randomly selected eleven primary schools in the Lithuanian capital, Vilnius, as model of a middle-size Eastern European city. Total PNC in the size range from 0.01 to >1.0 μm in diameter was measured using a condensation particle counter. Using an optical particle sizer, PNC was measured and PMC estimated for particles from 0.3 to 10.0 μm. A descriptive statistics was used to estimate the aerosol pollution levels. RESULTS: During all seasons, local cafeterias in the absence of ventilation were the main sources of the elevated levels of indoor PMC and PNC (up to 97,500 particles/cm). The other sources of airborne particulates were the children's activity during the lesson breaks with PMC up to 586 μg/m. Soft furniture, carpets in the classrooms and corridors were responsible for PMC up to 200 μg/m. Outdoor aerosol pollution (up to 18,170 particles/cm) was higher for schools in city center. Elevated air pollution in classrooms also resulted from intermittent sources, such as construction work during classes (200-1000 μg/m) and petrol-powered lawn trimmers (up to 66,400 particles/cm). CONCLUSION The results of our survey show that even in a relatively low polluted region of Eastern Europe there are big differences in aerosol pollution within middle-sized city. Additional efforts are needed to improve air quality in schools: more frequent wet cleaning, monitoring the operation of ventilation systems, a ban on construction works during school year, on a use of sandblasting mechanisms in the neighborhood of schools.