One of the enduring puzzles of atmospheric physics is the extent to which changes in the Sun can influence the behaviour of the climate system. While solar–flux changes tend to be relatively modest, a number of observations of atmospheric parameters indicates a disproportionately large response. Global–scale models of the coupled middle and upper atmosphere have provided new insights into some of the mechanisms that may be responsible for the amplification of the solar signal. In particular, modification of the transport of heat and chemicals such as ozone by waves during periods of solar activity has been shown to make an important contribution to the climate of the stratosphere and mesosphere. In this paper, a review of some of the recent advances in understanding the coupling between atmospheric layers and how this work relates to Sun–weather relations and climate change in the troposphere will be presented, along with a discussion of some of the challenges that remain.