The energy output of the Sun is modulated with a 11-year period known as the solar cycle. Increases in the solar ultra-violet (UV) and extreme ultra-violet (EUV) radiation output of the Sun during solar cycle maximum result in temperature, density and composition variations in the Earth's upper atmosphere. When the atmospheric density increases significantly at the altitude of orbiting spacecraft, the resultant increase in aerodynamic drag causes satellite orbits to decay more rapidly. Increased solar activity, therefore, effectively reduces the useful lifetime of spacecraft. Predicting the atmospheric density for several years ahead can be of great importance, since a mission's duration may be extended if launch takes place during a low density epoch. In addition to affecting launch date decisions, shorter time scale density variations and gusting winds can cause perturbations to an existing satellite's orbit, causing it to go off course. Such perturbations usually occur during periods of high geomagnetic activity. In this paper we review current knowledge of the effect of solar activity on the thermosphere and present data obtained by the Dynamics Explorer 2 spacecraft and model results from the National Center for Atmospheric Research, Thermospheric General Circulation Model, the illustrate the effect of increased solar and geomagnetic activity on composition, temperature and the dynamic structure of the upper atmosphere. We also show how subtle change in the interplanetary magnetic field (IMF) can affect the form of the neutral gas circulation at high latitudes, with important implications for polar orbiting spacecraft.