The formation of secondary organic aerosols (SOA) is simulated for the Nashville/western Tennessee domain using three recent SOA modules incorporated into the three-dimensional air quality model, CMAQ. The Odum/Griffin et al. and CMU/STI modules represent SOA absorptive partitioning into a mixture of primary and secondary particulate organic compounds (OC), with some differences in the formulation of the absorption process and the selection of SOA species and their precursors. Empirical representations based on measured laboratory SOA yields are used for condensable organic products in both these modules. The AEC module simulates SOA absorption into organic and aqueous particulate phases, and a representation based on an explicit gas-phase mechanism is used in the AEC module. Predicted SOA concentrations can vary by a factor of 10 or more. In general, the gas-phase mechanistic approach predicts a higher yield of SOA than those based on laboratory yields. There exist some differences in the two empirical modules despite their similar basis on experimental data. All three modules predict a dominance of SOA of biogenic origin as compared to SOA of anthropogenic origin. The causes for differences among the three SOA modules include the representation of terpenes, the mechanistic versus empirical representation of SOA-forming reactions, the identities of SOA, and the parameters used in the gas/particle partitioning calculations. Two sensitivity studies show that formation of water-soluble SOA and temperature dependence may be areas of key uncertainties affecting current models.