Inverse modelling is a useful tool for retrieving CH4 fluxes; however, evaluation of the applied chemical transport model is an important step before using the inverted emissions. For inversions using column data one concern is how well the model represents stratospheric and tropospheric CH4 when assimilating total column measurements. In this study atmospheric CH4 from three inverse models is compared to FTS (Fourier transform spectrometry), satellite and in situ measurements. Using the FTS measurements the model biases are separated into stratospheric and tropospheric contributions. When averaged over all FTS sites the model bias amplitudes (absolute model to FTS differences) are 7.4 ± 5.1, 6.7 ± 4.8, and 8.1 ± 5.5 ppb in the tropospheric partial column (the column from the surface to the tropopause) for the models TM3, TM5-4DVAR, and LMDz-PYVAR, respectively, and 4.3 ± 9.9, 4.7 ± 9.9, and 6.2 ± 11.2 ppb in the stratospheric partial column (the column from the tropopause to the top of the atmosphere). The model biases in the tropospheric partial column show a latitudinal gradient for all models; however there are no clear latitudinal dependencies for the model biases in the stratospheric partial column visible except with the LMDz-PYVAR model. Comparing modelled and FTS-measured tropospheric column-averaged mole fractions reveals a similar latitudinal gradient in the model biases but comparison with in situ measured mole fractions in the troposphere does not show a latitudinal gradient, which is attributed to the different longitudinal coverage of FTS and in situ measurements. Similarly, a latitudinal pattern exists in model biases in vertical CH4 gradients in the troposphere, which indicates that vertical transport of tropospheric CH4 is not represented correctly in the models.