Abstract. Reliable reference profiles and estimates of variability are a necessity for a variety of processes relating to ENVISAT including the development of key aspects and inputs for the operational processor for the Michelson Interferometer for Passive Atmospheric Sounding. MIPAS reference atmospheres have therefore been produced in two forms, namely standard atmospheres for modelling and error analysis for typical atmospheric situations and the IG2 seasonal climatologies for initial guess profiles used as part of the operational processing. The reference states cover 36 species on a common altitude, pressure, and temperature grid from 0 to 120 km, and include both means and estimates of variability (maximum, minimum and one sigma values). This paper describes V3.1 of the standard atmospheres and V4.0 of the IG2 atmospheres which are the current versions of the reference atmospheres. Particular attention is paid to the MIPAS operational geophysical products (pressure/temperature, H2O, O3, CH4, N2O, HNO3 and NO2) and to CO2 whose mixing ratio is required for the retrieval of pressure and temperature. A dynamic representation of CO2 is presented which shows the presence of CO2 gradients in the troposphere and the lower stratosphere. Since these atmospheres have been produced independently of MIPAS data, it is also possible to compare the data to the MIPAS operational products and derive valuable information on both the reference atmospheres and on MIPAS data products themselves. This process has been performed for V4.61/V4.62 data from the year 2003 as part of the MIPAS validation activity. It is demonstrated that the agreement between the MIPAS mean data and the reference atmospheres is very good in mid-latitudes and the tropics, verifying these data to first order. There is also reasonable agreement in standard deviations between the IG2 atmospheres and the corresponding sigmas calculated from the MIPAS data. Knowledge of tropospheric concentrations of CH4 and N2O is used to examine the accuracy of the MIPAS data and their susceptibility to cloud effects. It is shown that for the highest accuracy, MIPAS data should be filtered with cloud index values of 2.5 for N2O and 3.5 for CH4. Once such filtering has been performed, the MIPAS data for these species appear to be accurate to within 10% in the upper troposphere. The use of cloud index data in combination with MIPAS data is recommended for studies of the polar winter stratosphere and the upper troposphere/lower stratosphere.

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