This paper estimates the uncertainty in the outputs of a chemistry-transport model due to physical parameterizations and numerical approximations. An ensemble of 20 simulations is generated from a reference simulation in which one key parameterization (chemical mechanism, dry deposition parameterization, turbulent closure, etc.) or one numerical approximation (grid size, splitting method, etc.) is changed at a time. Intercomparisons of the simulations and comparisons with observations allow us to assess the impact of each parameterization and numerical approximation and the robustness of the model. An ensemble of 16 simulations is also generated with multiple changes in the reference simulation in order to estimate the overall uncertainty. The case study is a four-month simulation of ozone concentrations over Europe in 2001 performed using the modeling system Polyphemus. It is shown that there is a high uncertainty due to the physical parameterizations (notably the turbulence closure and the chemical mechanism). The low robustness suggests that ensemble approaches are necessary in most applications.