In November 2008, Svalbard Science Forum organised a workshop with the aim to discuss future focal areas in atmosphere research in Ny-Ålesund. The result is this document that initiates an Atmosphere Research Flagship programme as part of the NySMAC science plan for Ny-Ålesund. In Ny-Ålesund, long term measurements of several key climate parameters from the surface level up to the ozone layer have been performed for decades already. Such comprehensive data sets are available from very few sites in the Arctic and the data are continuously fed into global networks. Ny-Ålesund offers excellent conditions for scientific research, due to its accessibility and international and multidisciplinary character. For atmospheric research, Ny-Ålesund offers the possibility to perform continuous measurements both close at sea level and at 475 m of altitude within a relatively pristine environment. Also, its location under the magnetospheric cusp makes it a unique place for observing the solar wind and magnetosphere interaction on the dayside. In order to optimally use these excellent conditions for atmospheric research and to improve cooperation within the Kongsfjorden science community, this document describes general flagship goals which include the optimal utilization of available instruments and data sets, the establishment and further development of common research infrastructures, and a programme to investigate the representativeness of measurements in Ny-Ålesund for climate change research and atmospheric process studies. The flagship programme states the following future research priorities: • Long term observations of key parameters concerning climate change • Planetary boundary layer (PBL) research • Studies and monitoring of long range transport of pollutants • Arctic ozone layer and UV research • Ionospheric / magnetospheric research • Validation and synergistic analyses of satellite data The flagship programme aims to establish a unique international long-term atmospheric monitoring and observation platform supported by all research institutions represented in Ny-Ålesund and thus to realize a supersite, allowing investigations of the complex Arctic System with a multidisciplinary approach. Interdisciplinary observations will be performed elucidating interaction processes on sea, snow and ice surfaces and the atmosphere. Special emphasis will be laid upon the impact of climate change on the Arctic environment. Furthermore, means of better integration of atmospheric research within NyÅlesund, Svalbard as well as on a circumpolar level are discussed, and possibilities for interdisciplinary cooperation with other flagships are pointed out. Finally, three appendices give an overview of atmospheric stations in Ny-Ålesund, atmospheric parameters measured in Ny-Ålesund, and the atmospheric monitoring satellites in operation in 2010–2020.