This special issue of Science and Public Policy takes up the recently discussed problem of political coordination in the ‘third phase of innovation’. The introduction prepares the analytical ground for the four case studies that follow. It develops the image of a ‘knowledge space’ consisting of the four ‘core’ areas of innovation policy — higher education, professional education, basic research and technological research — and uses insights from administrative science and a number of science and policy studies that discuss the need for coordination in policy-making in knowledge and innovation systems. Different types of coordination are distinguished as well as various institutional levels within the political system that play a role in the overall capacity of improving political coordination. A number of problems and expectations are raised which are the starting point of reflections in the ensuing case studies.