Mechanical ventilation of buildings is a risk factor for building related symptoms (BRS). This analysis examines air filters within mechanical ventilation systems to determine their effect on BRS. We hypothesize that certain ventilation filter materials will contribute more than others to the burden of building related headaches, mucous membrane (MM) and lower respiratory (LR) BRS within a building. This hypothesis was tested using the US EPA Building Assessment, Survey and Evaluation (BASE) study. Logistic regression models constructed to control for personal, workplace, and environmental factors reveled statistically significant (p<0.05) associations between the increased prevalence of building related headaches, certain MM and LR BRS and polyester or synthetic containing air filters in a ventilation system, relative to fiberglass or cotton air filters.