Alternative housing systems impact indoor air quality differently. The Coalition for Sustainable Egg Supply (CSES) study monitored indoor air quality over a 27-month period among three housing systems to quantify indoor gaseous and particulate matter (PM) concentrations, thermal environment and building ventilation rates. A mobile air emission-monitoring unit (MAEMU) was used to collect and analyze air samples from three locations per house and one ambient location. Aviary houses had a difficult time maintaining temperature compared to conventional caged and enriched colony systems and were found to have poorer indoor air quality with higher ammonia levels, PM levels and carbon dioxide concentrations. Methane concentrations were similar for all three housing types and there was no significant difference in relative humidity.