With the increased utilization of school buildings on a year-round basis, school indoor air quality has become a national concern. The purpose of this study was to evaluate possible associations between ventilation system type and occupant perception of indoor air quality. Staff (n = 403) from 12 schools completed a self-administered questionnaire. Carbon dioxide (CO2) levels, air exchange rates, and particle counts were also measured for each school. Schools with unit ventilator (UV) systems had the lowest mean CO2 level at 637 ppm, followed by the variable air volume (VAV) systems with 664 ppm, and constant volume (CV) systems with a mean of 703 ppm. Schools with UV systems had the lowest mean air exchange rate at 2.67 air changes per hour (ACH), followed by the VAV system type at 2.80 ACH and the CV system type at 4.61 ACH. Indoor versus outdoor particle ratios were calculated for each ventilation system type. Particles with aerodynamic diameters ranging from 0.1-1.0 microm had a geometric mean ratio ranging from 0.38 to 0.68; particles with aerodynamic diameters ranging from 1-3 microm had ratios ranging from 1.39 to 5.47, and particles with aerodynamic diameters greater than 3 microm had ratios ranging from 3.20 to 14.76. Schools using VAV systems had a significantly lower prevalence of red and watery eyes while schools with UV systems had an elevated prevalence of nasal congestion, sore throat, headache, and dustiness complaints. This increased prevalence of complaints in buildings with UV systems may be due to the increased particulate levels.