To examine the association between indoor classroom conditions and student illness-related absenteeism (IRA) under different seasonal conditions, around 1900 students from 85 elementary classrooms were enrolled in a year-long study. Various indoor air quality (IAQ) and thermal conditions (TC) were repeatedly monitored during a school year. Student IRA rates were separately examined during heating and cooling seasons. By using negative binomial models, some associations were observed. During the cooling season, an additional 1,000,000 particles/L with aerosol diameter less than 2.5 μm corresponded with a 3% increase of IRA. During the heating season, no association with aerosol particles was observed, but a 100 ppm increase of carbon dioxide concentration in the supply air was associated with 3% increase of IRA with statistical significance. Additional investigation is needed to understand the mechanisms and other potential confounding factors in these associations.