Mesosphere – stratosphere transport during Southern Hemisphere autumn (March–June 2003) is studied using a pole-centred approach of along-orbit sequences of vertical profiles of methane observations from the Envisat MIPAS (Michelson Interferometer for Passive Atmospheric Sounding) instrument suppl1emented by meteorological analyses from ECMWF and the Met Office. We hypothesize that the methane distribution can be explained as a combination of two transport processes: (1) isentropic transport in the lower mesosphere and upper stratosphere of methane-rich air from low/mid latitudes to high latitudes during early autumn, and (2) diabatic descent at high latitudes of methane-poor air from the lower mesosphere during autumn. Calculations of stratospheric effective diffusivity provide broad support for this hypothesis. The along-orbit data are shown to provide more information than studies using spatial and temporal averages of the same MIPAS methane data, and to explain anomalous features in the methane distribution, where the vertical gradient is reversed, reported by studies using MIPAS and ILAS-II data. Copyright © 2009 Royal Meteorological Society