The analytical framework of regional innovation systems highlights the systemic nature of regional economies and the need for policy coordination within regions. Coordination presupposes an understanding of the underlying problems that may act as barriers to regional development. Three generic problems facing regions are: lack of resources (e.g. human and financial capital), negative lock-in (e.g. to historically strong sectors), and fragmentation of actors and activities. There are only a few examples of innovation system studies that investigate these problems by analysing actors and their activities as well as the institutional framework surrounding them. This paper offers a framework for analysing innovation system problems, focusing on actors and activities as well as institutions. In doing so, the need for coordination of activities performed by different actors is highlighted, as is the relevance of neutrality in the coordinating function. Three sectoral policy initiatives in a Swedish region are studied.