We present a new three-dimensional chemistry-climate model (CCM) called the “Meteorological Research Institute (MRI) Chemistry-Climate Model, version 2” (MRI-CCM2). The model treats chemical and physical processes interactively from the surface to the stratosphere to simulate the global distribution and evolution of ozone and other trace gases with a framework similar to that of version 1 (MRI-CCM1), which was a stratospheric model. We have added detailed tropospheric chemistry to Version 1 in order to seamlessly treat ozone chemistry in both the troposphere and stratosphere. The chemistry module of Version 2 includes 90 chemical species with 172 gas-phase reactions, 59 photolysis reactions and 16 heterogeneous reactions; includes improved grid-scale transport with a semi-Lagrangian scheme, sub grid-scale convective transportand turbulent diffusion, dry and wet deposition, and emissions of trace gases from various sources. We conducted a free run and an assimilated run towards observed atmospheric fields over 11 years, to reproduce the 1990s distribution of chemical constituents. The simulated seasonal cycle and geographical distribution of ozone below the middle troposphere are generally in good agreement with ozonesonde observations, although ozone was underestimated in the lower troposphere in the south polar region, and extratropical ozone was overestimated in the upper troposphere and lower stratosphere. Version 2 also reproduces realistic characteristics for other species such as carbon monoxide (CO), nitric oxide (NO), and the hydroxyl radical (OH): The model reproduces the observed seasonal cycle of CO well, although it overestimates CO by about 15 ppbv in the southern high latitudes; the vertical profiles of NO captures the observed features; and finally, distribution of the OH radical is similar to that simulated by other recent CCMs.