This paper presents the intercomparison of O3, HNO3, ClO, N2O and CO profiles measured by the two spaceborne microwave instruments MLS (Microwave Limb Sounder) and SMR (Submillimetre Radiometer) on board the Aura and Odin satellites, respectively. We compared version 1.5 level 2 data from MLS with level 2 data produced by the French data processor version 222 and 225 and by the Swedish data processor version 2.0 for several days in September 2004 and in March 2005. For the five gases studied, an overall good agreement is found between both instruments. Most of the observed discrepancies between SMR and MLS are consistent with results from other intercomparison studies involving MLS or SMR. O3 profiles retrieved from the SMR 501.8 GHz band are noisier than MLS profiles but mean biases between both instruments do not exceed 10%. SMR HNO3 profiles are biased low relative to MLS's by ~30% above the profile peak. In the lower stratosphere, MLS ClO profiles are biased low by up to 0.3 ppbv relative to coincident SMR profiles, except in the Southern Hemisphere polar vortex in the presence of chlorine activation. N2O profiles from both instruments are in very good agreement with mean biases not exceeding 15%. Finally, the intercomparison between SMR and MLS CO profiles has shown a good agreement from the middle stratosphere to the middle mesosphere in spite of strong oscillations in the MLS profiles. In the upper mesosphere, MLS CO concentrations are biased high relative to SMR while negative values in the MLS retrievals are responsible for a negative bias in the tropics around 30 hPa.