People spend most of their time in indoor environments and, consequently, these environments are more significant for the contribution of the daily pollutant exposure than outdoors. In case of children, a great part of their time is spent at school. Therefore, evaluations of this microenvironment are important to assess their time-weighted exposure to air pollutants. The aim of this study was to assess the children exposure to bioaerosols at schools from two different types of areas, urban and rural. A methodology based upon passive sampling was applied to evaluate fungi, bacteria and pollens, simultaneously with active sampling for fungi and bacterial assessment. Results showed very good correlations between sampling methods, especially for summer season. Passive sampling methodologies presented advantages such as no need of specific and expensive equipment, and they allow achieving important qualitative information. The study was conducted in different periods of the year to study the seasonal variation of the bioaerosols. Fungi and pollen presented higher levels during the summer time whereas bacteria did not present a seasonal variation. Indoor to outdoor ratios were determined to assess the level of outdoor contamination upon the indoor environment. Levels of fungi were higher outdoor and bacteria presented higher concentrations indoors. Indoor levels of bioaerosols were assessed in primary schools of urban and rural areas, using the active method along with a passive sampling method. Very good correlations between methods were found which allow the use of the passive sampling method to supply important and reliable qualitative information of bioaerosols concentrations in indoor environments. Seasonal variation in bioaerosols concentrations were found for fungi and pollen. Concentrations of fungi and bacteria above AMV (Acceptable Maximum Value) were found for most of the studied classrooms showing the importance of this microenvironment for the high exposure of children to bioaerosols.