A three-dimensional, time-dependent, coupled model of the thermosphere and ionosphere has been used to assess the influence of proton auroral precipitation on Earth's upper atmosphere. Statistical patterns of auroral electron and proton precipitation, derived from DMSP satellite observations, have been used to drive the model. Overall, electrons are the dominant particle energy source, with protons contributing ~15% of the total energy. However, owing to the offset of the proton auroral oval toward dusk, in certain spatial regions protons can carry most of the energy. This is the case particularly at the equatorward edge of the dusk sector and at the poleward edge of the dawn sector of the auroral oval. The increase in Pedersen conductivity raises the average Joule heating by ~10%, so raising the E and F region temperature by as much as 7%. The enhanced E region ionization also drives stronger neutral winds in the lower thermosphere through ion drag, which alters the temperature structure through transport, adiabatic heating, and adiabatic cooling. The neutral wind velocity modifications in the E region can reach 40% in some sectors. In addition, the upwelling of neutral gas raises the N2/O ratio, depleting the F region and so reducing the ion-drag driven winds in this region. This study illustrates the modest yet significant impact of auroral proton precipitation on the upper atmosphere. ¿ 2001 American Geophysical Union