Recent developments in observational techniques and the extension of observational networks have enabled the capture of atmospheric phenomena concurrently over a wide range of temporal and spatial scales. In addition, global numerical models, including coupled climate models and chemistry climate models, in which data assimilation techniques are implemented, are being extended to higher-altitude regions with greater horizontal and vertical resolutions. These developments allow the examination of atmospheric phenomena over a wide range of temporal and spatial scales in terms of their interactions and momentum/energy budgets. Such observations and models generate considerable amounts of data; thus, methods of data analysis are becoming increasingly important and ”data-centric” science needs to be pursued. In parallel, new theories that can treat various phenomena seamlessly and three-dimensionally are needed, and those able to describe inductively elucidated structures are being constructed. With these circumstances in mind, the International Symposium on the Whole Atmosphere (ISWA) was organized and held on 14-16 September 2016 (http://pansy.eps.s.u-tokyo.ac.jp/iswa/) in order to review the latest research regarding the whole atmosphere. The symposium included particular focus on the dynamics of the middle and upper atmosphere, and discussion on the direction of future research. To share the new and valuable knowledge discussed among the participating communities during the symposium, we have issued this Special Edition on International Symposium on the Whole Atmosphere (ISWA) in SOLA.