A one-day workshop on "Plant Roots" was organised by the GIS BV and the AllEnvi Alliance in Montpellier on February 27 th 2012. It brought together 45 scientists and laboratory representatives from the French public and private research community. The workshop demonstrated the strength of the French research community, originating from various research organisations and areas of expertise, in this internationally competitive research field. The position paper reflects the presentations and discussions of the "Plant Roots" workshop and summarizes the areas of research to which the French public and private research community would be particularly fit to contribute, through trans-disciplinary and translational projects. This position paper is endorsed by the Governing Council of the GIS BV and by the working group"Plant Biology and Biotechnologies" of the AllEnvi Alliance.