This paper discusses the present understanding of ionospheric storms, in particular storm effects in the F-layer and their relationship to changes of thermospheric composition. After summarizing the main effects of storms on the F-layer and the neutral thermosphere, the paper discusses some recent theoretical modelling of how the thermosphere responds to energy inputs at high latitudes, such as occur during storms. The high-latitude inputs set up a thermospheric “storm circulation”, with consequent world-wide temperature increases and changes in chemical composition. These composition changes appear quite differently when viewed at fixed heights and at fixed pressure-levels. At fixed heights in the F-layer, there are marked increases of neutral molecular/atomic concentration ratio; but at fixed pressure-levels the increases are confined to high latitudes, with decreases at middle and low latitudes. The results of the modelling cast doubt on the theory that negative F-layer storms at midlatitudes are caused by decreases in the atomic/molecular ratio brought about by dynamical processes originating at high latitudes. The implications for storm theories, and alternative mechanisms for producing negative storm effects, are discussed. It is still considered that the negative storm effects are probably due to photochemical processes. The possibilities include widespread enhancement of the vibrational excitation of molecular nitrogen, induced by soft particle precipitation, or substantial energy inputs at latitudes well equatorward of the auroral ovals.