The chemical composition of the mixing layer above the tropopause, which is mainly influenced by stratosphere troposphere exchange, impacts the chemistry and radiative balance of the troposphere. A better understanding of its seasonal and spatial variation is needed to reduce uncertainties of global chemistry-transport models. In this paper, we use the Measurements of Ozone, Water Vapour, Nitrogen Oxides and Carbon Monoxide by Airbus In-Service Aircraft (MOZAIC) ozone and carbon monoxide data from 2003. The five MOZAIC aircraft fly daily between Europe and North America and between Europe and Asia, at 9–12 km crossing the tropopause when transecting upper level troughs. We present a new coordinate system consisting of potential vorticity on the y axis and the angle between the local PV surface and the horizontal on the x axis to study the mixing that occurs in the tropopause region. This coordinate system allows us to view the typical distribution of ozone and CO within upper level troughs. Using in situ measurements and a Lagrangian analysis, we have identified a mixing layer associated with stirring and mixing in the tropopause region between 2 and 6 pvu. Regional variations of the ozone and CO distributions and chemical anomalies between the center and the borders of the upper level troughs are found within the mixing layer.