Within their domain, regional climate and weather forecasting models deviate from the driving data. Small-scale deviations are a desired effect of adding regional details. There are, however, also deviations of the large-scale circulation, which can be caused by orographic effects and depend on the large-scale flow condition. These ‘secondary circulations’ (SCs) are confined to the model domain due to the prescribed boundary conditions. Here, the impact of different regional model configurations on the SC is analysed in a case study for the European region using an ensemble approach. It is shown that at 500 hPa, vortices of the SC have diameters on the order of several thousand kilometres and are related to wind speed anomalies of more than 5 m/s and geopotential height anomalies of more than 5 dam. The spatial structure and the amplitude of the SC strongly depend on the location of the lateral boundaries. The impact of the boundary location on the anomalies is on the same order of magnitude as the anomalies themselves. The resolution of the regional model, as well as the application of spectral nudging and a smoothed topography, affects mainly the amplitude of the SC, but not the spatial structure.