Despite their important role in shaping the technologies of the future, public research and development (R&D) programmes are rarely based on systematic assessments of the environmental effects. R&D programmes thus allocate a huge amount of financial resources to projects, which potentially may cause severe negative environmental impacts. This paper presents an innovative environmental assessment practice on R&D programmes in Denmark. It reports on the challenges and experiences of assessing the Danish R&D programme ForskEL, which promotes R&D projects within the electricity sector. The programme is characterised by uncertainty about impacts and incomparable project types and technologies. A methodology for dealing with these challenges is presented, and experiences from a testing of the methodology on the 2012 programme are reflected upon. Finally the assessment is discussed in terms of its potential for making a difference for the future development and deployment of renewable energy.