Abstract. Simulations of the Martian upper atmosphere have been produced from a self-consistent three-dimensional numerical model of the Martian thermosphere and ionosphere, called MarTIM. It covers an altitude range of 60 km to the upper thermosphere, usually at least 250 km altitude. A radiation scheme is included that allows the main sources of energy input, EUV/UV and IR absorption by CO₂ and CO, to be calculated. CO₂, N₂ and O are treated as the major gases in MarTIM, and are mutually diffused (though neutral chemistry is ignored). The densities of other species (the minor gases), CO, Ar, O₂ and NO, are based on diffusive equilibrium above the turbopause. The ionosphere is calculated from a simple photoionisation and charge exchange routine though in this paper we will only consider the thermal and dynamic structure of the neutral atmosphere at solar minimum conditions. The semi-diurnal (2,2) migrating tide, introduced at MarTIM's lower boundary, affects the dynamics up to 130 km. The Mars Climate Database (Lewis et al., 2001) can be used as a lower boundary in MarTIM. The effect of this is to increase wind speeds in the thermosphere and to produce small-scale structures throughout the thermosphere. Temperature profiles are in good agreement with Pathfinder results. Wind velocities are slightly lower compared to analysis of MGS accelerometer data (Withers, 2003). The novel step-by-step approach of adding in new features to MarTIM has resulted in further understanding of the drivers of the Martian thermosphere.