Our group previously demonstrated that carbon dioxide (CO2) levels in heavily occupied schools correlate with the levels of airborne bacterial markers. Since CO2 is derived from the room occupants, it was hypothesized that in schools, bacterial markers may be primarily increased in indoor air because of the presence of children; directly from skin microflora or indirectly, by stirring up dust from carpets and other sources. The purpose of this project was to test the hypothesis. Muramic acid (Mur) is found in almost all bacteria whereas 3-hydroxy fatty acids (3-OH FAs) are found only in Gram-negative bacteria. Thus Mur and 3-OH FA serve as markers to assess bacterial levels in indoor air (pmol m(-3)). In our previous school studies, airborne dust was collected only from occupied rooms. However, in the present study, additional dust samples were collected from the same rooms each weekend when unoccupied. Samples were also collected from outside air. The levels of dust, Mur and C10:0, C12:0, C14:0, and C16:0 3-OH FAs were each much higher (range 5-50 fold) in occupied rooms than in unoccupied school rooms. Levels in outdoor air were much lower than that of indoor air from occupied classrooms and higher than the levels in the same rooms when unoccupied. The mean CO2 concentrations were around 420 parts per million (ppm) in unoccupied rooms and outside air; and they ranged from 1017 to 1736 ppm in occupied rooms, regularly exceeding 800-1000 ppm, which are the maximum levels indicative of adequate indoor ventilation. This indicates that the children were responsible for the increased levels of bacterial markers. However, the concentration of Mur in dust was also 6 fold higher in occupied rooms (115.5 versus 18.2 pmole mg(-1)). This further suggests that airborne dust present in occupied and unoccupied rooms is quite distinct. In conclusion in unoccupied rooms, the dust was of environmental origin but the children were the primary source in occupied rooms.