The first simulations of stratospheric chemistry using the Chemical Lagrangian Model of the Stratosphere (CLaMS) are reported. A comprehensive chemical assimulation procedure is described that combines satellite, airborne, and balloon-borne tracer observations with results from a two-dimensional photochemical model simulation. This procedure uses tracer-tracer and tracer-potential vorticity mapping techniques. It correctly reproduces all basic features of the observed tracer distribution. This methodology is used to generate the initial composition fields that will be used for subsequent chemical simulations. Results from a 6-day simulation starting on 20 February 1997 show that the simulated HNO3 distribution displays the correct morphology, although the extremes of the observed HNO3 distribution are underestimated. The simulated ClO distribution exhibits a similar morphology to the observed Microwave Limb Sounder ClO distribution. Because of unseasonally low temperatures in the arctic lower stratosphere during spring 1997, high levels of chlorine activation are maintained in the simulation, resulting in up to 1.8 ppmv of chemical ozone loss over a 5-week period. Furthermore, simulations show strong spatially inhomogeneous chemical ozone depletion within the polar vortex and show that greatest ozone loss is confined to the vortex core. These results are confirmed by several Halogen Occultation Experiment and ozone sonde profiles, although the minimum ozone concentrations are overestimated. These studies demonstrate that CLaMS is capable of simulating vortex isolation, an essential feature of the polar vortex.