The Children's Environment and Health Action Plan for Europe (CEHAPE) of WHO focuses (inter alia) on improving indoor environments where children spend most of their time. At present, only little is known about air pollution in schools and its effect on the lung function of school children. Our project was set up as an Austrian contribution to CEHAPE. In a cross-sectional approach, differences in indoor pollution in nine elementary all-day schools were assessed and 34 of these pollutants were analyzed for a relationship with respiratory health determined by spirometry using a linear regression model. Overall 596 children (aged 6–10 years) were eligible for the study. Spirometry was performed in 433 children. Socio-economic status, area of living (urban/rural), and smoking at home were included in the model as potential confounders with school-related average concentration of air pollutants as the variable of primary interest. A negative association with flow volumes (MEF₇₅) was found for formaldehyde in air samples, benzylbutylphthalate and the sum of polybrominated diphenylethers in school dust. FVC and FEV₁ were negatively associated with ethylbenzene and xylenes in air samples and tris(1,3-dichlor-2-propyl)-phosphate on particulates. Although, in general, the quality of school indoor air was not worse than that reported for homes, effects on the respiratory health of children cannot be excluded. A multi-faceted strategy to improve the school environment is needed.