Aims: This paper examines the role of organizational structure within government(s) in attempts to implement intersectoral action for health in Danish municipalities. We discuss the implications of structural reorganization and the governance structures that are established in order to ensure coordination and integration between policy sectors. Methods: The paper is based on 49 interviews with civil servants from health and non-health sectors of 10 municipalities. Based on participants’ experiences, cases have been described and analyzed in an iterative process consulting the literature on Health in All Policies and joined-up government. Results: Continuous and frequent processes of reorganizing were widespread in the municipalities. However, they appeared to have little effect on policy change. The two most common governance structures established to transcend organizational boundaries were the central unit and the intersectoral committee. According to the experiences of participants, paradoxically both of these organizational solutions tend to reproduce the organizational problems they are intended to overcome. Even if structural reorganization may succeed in dissolving some sector boundaries, it will inevitably create new ones. Conclusions: It is time to dismiss the idea that intersectoral action for health can be achieved by means of a structural fix. Rather than rearranging organizational boundaries it may be more useful to seek to manage the silos which exist in any organization, e.g. by promoting awareness of their implications for public health action and by enhancing the boundary spanning skills of public health officers.