The air quality model (AQM) package SAIMM/UAM-V Systems Applications International Mesoscale Model/Urban Airshed Model with Variable grid was applied to a domain with complex topography including Switzerland. The output pressure at a fixed height above sea level generated by one of the SAIMM post-processor showed unexpected variations of about 40 hPa over the domain. We found that these fluctuations were caused by an incorrect definition of the pressure reference height. After the change of this definition, realistic pressure values were obtained. Using the correct pressure field as input, we simulated the 3-dimensional mixing ratios of pollutants with UAM-V for the summer smog period of July 28-29, 1993. The values tended to increase with height above the surface and with surface elevation above sea level. The Swiss topography was mirrored in the mixing ratio fields. By using CO as a quasi-inert tracer, it became evident that transport phenomena such as advection and diffusion did not consider expansions or compressions due to pressure and temperature variations. After the conversion of the concentrations to a common reference pressure and temperature before the calculation of transport, these strange topographic features in the mixing ratios vanished completely. The CO mixing ratio was underestimated by 10-15 ppb (7-10%) in the lowest layer over the Swiss Plateau due the omission of compression or expansion. For O 3 and NO 2 , the differences were 0-5 ppb (0-10%) and 0-0.2 ppb (0-15%), respectively.