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In this study, atmospheric aerosol concentration levels in two schools (a primary and a secondary grammar) and a kindergarten were investigated. The selected institutions are located close to the center of Debrecen, where the traffic density is rather high. Coarse and fine mass concentrations (PM), elemental composition and mass size distributions were determined in the selected microenvironments. These were different classrooms, school yards, gymnasiums, a computer lab, a chemical lab and a so-called salt room. The elemental composition (for Z ≥ 13) was determined by PIXE. In all cases, the coarse concentrations of PM were found to be higher inside the educational buildings than in the outer air. In every case, the indoor PM 10 concentrations exceeded the EU air quality standard. The fine and coarse elemental concentrations did not exhibit marked variability in the selected microenvironments. On the basis of the mass size distribution, we found significant differences between the two rooms of the kindergarten. On the basis of the mass size distribution data, a stochastic lung deposition model was used to calculate the total and regional deposition efficiencies of the different types of particles along the human respiratory system.