We have used two different General Circulation Models to study the thermal and wind structure of the Martian upper atmosphere (mesosphere and thermosphere). Both models take into account the effects of waves propagating from the lower atmosphere, although they use different methods for this purpose. We present the results of three simulations that allow us to take into account the seasonal variability of the Martian atmosphere. Simplified dust scenarios and a common set of input parameters are used. The temperatures and winds predicted by both models show an overall good agreement. However, some differences have been identified, generally of a local nature. The magnitude of these differences tends to increase with the amount of dust in the lower atmosphere. The different heating terms of the upper atmosphere predicted by both models are in good agreement, which suggests that the differences between the models have their origin in the propagation of waves from the lower atmosphere. This study has allowed us to confirm the important role of the redistribution of the energy by the winds in producing the longitude-latitude structure of the temperatures. Both models predict also a thermospheric polar warming during the Southern summer solstice, although its intensity seems to be model-dependent and connected to lower atmosphere dust loading.