A three‐dimensional radiative‐dynamical‐chemical model has been used to investigate measurements of column ClONO2 and HNO3 made by the airborne Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) instrument. MIPAS made measurements from the Transall aircraft in the northern hemisphere lower stratosphere from December 1992 to March 1993. The three‐dimensional model has a detailed stratospheric chemistry scheme including heterogeneous reactions on polar stratospheric clouds and sulfate aerosols. The circulation in the model is specified from the European Centre for Medium Range Weather Forecasts analyses. The MIPAS measurements reveal large variability in column ClONO2 at the edge of the polar vortex. For the measurements of January 27 and 31, 1993, the model experiments show that variability in ClONO2 observed over this period can be explained by polar stratospheric cloud processing and recovery. Measurements of ClONO2 on February 2, 1993, showed large variations depending on the orientation of the aircraft relative to the edge of the vortex. Results from the model show that this is qualitatively consistent with the aircraft flying near to the collar region with its associated strong horizontal gradients of ClONO2. The model's ability to simulate these strong gradients is limited by its relatively coarse resolution. In early March the vortex became very distorted. During this period MIPAS measured very large values of ClONO2 at high latitudes within the vortex but lower, although still large, values in the more southerly regions of the vortex. At this stage of the winter ClONO2 is the major chlorine species in the model at high latitudes. The model shows how the distortion of the vortex in March led to relatively high columns of ClONO2 in vortex air over southern Europe. The model also reproduces the observed gradient in ClONO2 within the vortex, and experiments show that these gradients are due, at least in part, to the availability of sunlight. This variability of ClONO2, and therefore active chlorine (ClOχ), implies that these tracers do not correlate well with potential vorticity. This places limitations on extrapolating localized measurements of anything but the longest lived chemical tracers to the whole of the polar vortex using potential vorticity, or indeed a long‐lived tracer, as part of a coordinate system.