This paper discusses the representation of chemistry in the Community Earth System Model (CESM), using the CAM4 physics and dynamics. We present a variety of configurations for the representation of tropospheric and stratospheric chemistry, wet removal, and online and offline meteorology. Results from simulations illustrating these configurations are compared with surface, aircraft and satellite observations. Overall, the model-data comparison indicates that the offline simulation driven by GEOS5 meteorological analyses provides the best simulation, possibly due in part to the increased vertical resolution (52 levels instead of 26 for online dynamics).