The Institute of Atmospheric Physics of the ASCR organised the 4th IAGA/ICMA/CAWSES-II TG4 Workshop on Vertical Coupling in the Atmosphere-Ionosphere System, which was held from 14–18, 2011 in Prague. The Earth’s atmospheric regions are intricately coupled to one another via various dynamical, chemical, and electrodynamic processes. However, the manner in which the couplings take place due to varying energy inputs from the Sun and from the lower atmosphere is a question that is yet to be understood.