Systemic policy instruments are receiving increased attention among innovation scholars as a means to stimulate sustainability oriented technological innovation. The instruments are called systemic in the expectation that they will improve the functioning of entire (innovation) systems. A first step in designing systemic instruments is an analysis of the systemic problems that hinder the development of a specific technological trajectory. This paper argues that two approaches to studying innovation systems—structural and functional analyses—can be combined in a systemic policy framework that helps to first, identify the systemic problems; and second, to suggest the systemic instruments that would address these problems.