The EISCAT (European Incoherent SCATer) Scientific Association has provided versatile incoherent scatter (IS) radar facilities on the mainland of northern Scandinavia (the EISCAT UHF and VHF radar systems) and on Svalbard (the electronically scanning radar ESR (EISCAT Svalbard Radar) for studies of the high-latitude ionised upper atmosphere (the ionosphere). The mainland radars were constructed about 30 years ago, based on technological solutions of that time. The science drivers of today, however, require a more flexible instrument, which allows measurements to be made from the troposphere to the topside ionosphere and gives the measured parameters in three dimensions, not just along a single radar beam. The possibility for continuous operation is also an essential feature. To facilitatefuture science work with a world-leading IS radar facility, planning of a new radar system started first with an EU-funded Design Study (2005–2009) and has continued with a follow-up EU FP7 EISCAT_3D Preparatory Phase project (2010–2014). The radar facility will be realised by using phased arrays, and a key aspect is the use of advanced software and data processing techniques. This type of software radar will act as a pathfinder for other facilities worldwide. The new radar facility will enable the EISCAT_3D science community to address new, significant science questions as well as to serve society, which is increasingly dependent on space-based technology and issues related to space weather. The location of the radar within the auroral oval and at the edge of the stratospheric polar vortex is also ideal for studies of the long-term variability in the atmosphere and global change. This paper is a summary of the EISCAT_3D science case, which was prepared as part of the EU-funded Preparatory Phase project for the new facility. Three science working groups, drawn from the EISCAT user community, participated in preparing this document. In addition to these working group members, who are listed as authors, thanks are due to many others in the EISCAT scientific community for useful contributions, discussions, and support.