Abstract Background Indoor Air Quality (IAQ) in schools is a public health concern, given the vulnerability of children as a demographic group and substantial amount of time that they spend in (highly occupied) classrooms. Conditions specific for school buildings, as well as location and outdoor air quality (OAQ), can adversely affect IAQ and children’s health. The aim of this study was to examine the seasonal variation in IAQ and the influence of OAQ herein in primary schools. Methods Sampling was carried out in summer and winter in 5 schools in central Poland. A culture-dependent method using impactors was applied to examine the total number of bacteria and fungi. Gas chromatography with flame ionization detector (quartz filters for sampling) was applied to determine concentrations of 16 polycyclic aromatic hydrocarbons (PAHs), crucial for their health impact. Results In poorly ventilated classrooms bacteria levels exceeded that of fungi. Bacterial contamination decreased in efficiently ventilated rooms, and before/after the lessons. In summer fungi concentration in indoor air was higher than in winter and reached the level of fungi outdoors. PAHs concentrations (especially those with 4 and more rings, which are biologically active) and the mutagenicity and carcinogenicity equivalents were elevated in winter and related to changes in concentrations in outdoor air. Conclusions IAQ in schools depends on a season. Occupants in classrooms are the main source of bacteria, but the type and number of microorganisms also depend on ventilation conditions. PAHs characteristic of coal/wood combustion indicates that in the absence of internal emission sources, external sources most likely affect IAQ in schools in winter.