A computer simulation tool, named "CHAMPS-Multizone," is introduced in this article for analyzing both energy and indoor air quality (IAQ) performance of buildings. The simulation model accounts for the dynamic effects of outdoor climate conditions (solar radiation, wind speed and direction, and contaminant concentrations), building materials and envelope system design, multi-zone air and contaminant flows in buildings, internal heat and pollutant sources, and operation of the building HVAC systems on the building performance. It enables combined analysis of building energy efficiency and indoor air quality The model also has the ability to input building geometry data and HVAC system operation related information from software, such as Sketch Up and DesignBuilder via IDF file format. A "bridge" to access static and dynamic building data stored in a "Virtual Building" database is also developed, allowing convenient input of initial and boundary conditions for the simulation and for comparisons between the predicted and measured results. This article summarizes the mathematical models, adopted assumptions, methods of implementation, and verification and validation results. The needs and challenges for further development are also discussed.