Ionospheric and thermospheric storms are strong perturbations in the ionosphere and thermosphere caused by the significant variations in the magnetic activity. The storms are quite complex phenomena and are not well understood yet. Simultaneous use of multiple instruments, both space-borne and ground-based, has already shown its great advantage in finding new aspects of the global distribution of the upper atmosphere plasma with unprecedented detail. One of the most interesting recent findings is the demonstration of an altitudinal difference of the ionospheric behavior during geomagnetic storms, and occurrence of intensive ionospheric irregularities in the topside ionosphere (above the ionization maximum). Here, we show several examples of the multi-instrumental analysis of the ionospheric and thermospheric effects during geomagnetic storms occurred within the last solar cycle.