Formal and informal institutions help shape processes of planning, as 'rules of the game'. However, institutions do not always align. As a result of changes in strategy and operation, institutional incongruence can emerge as old and new institutions conflict or as actors perceive and apply institutions in a different manner. In this article, we aim to gain insight in the concept of institutional incongruence and the way it shapes transport planning policy and implementation. To this end, we analyse the role of institutional congruence in the case of land use transport integration (LUTI) in the Netherlands. Although LUTI creates opportunities for beneficial synergies and helps avoid unwanted consequences, such as project time and project cost overruns, examples of successful deployment remain scarce. Through an institutional analysis of the Dutch national Planning, Programming and Budgeting (PPB) System for road infrastructure, we assess the ways in which LUTI is enabled or obstructed by formal and informal institutions. The one-year research project involves a triangulation of literature research, policy analysis, 22 expert interviews, focus groups and workshops. The findings illustrate that strategy and operation each present distinct formal and informal institutional incongruence that negatively influence land-use transport integration. We conclude that institutional incongruence is several instances of institutional incongruence can be found throughout the Dutch national planning process. These are partly inevitable because institutional change occurs gradually to reflect developments in society and manifests itself in both formal and informal rules. Therefore we recommend that, in order to achieve LUTI, the full institutional configuration of formal and informal rules, at strategic and operational level should be analysed, redesigned and aligned.