This paper presents actions for annulment as indicator for conflict over policy application in the EU and argues that it is a valuable complement to the indicator of infringement proceedings. This is because annulment actions shed light on conflicts in areas that remain undetected by infringement proceedings and because annulment actions are able to uncover potential multilevel characters of these conflicts. On this basis, the paper identifies four different types of multilevel application conflicts. Based on an original dataset on all actions for annulment initiated against the European Commission between 1957 and 2009, the paper explores the dominant cleavage structure in application conflicts over time. This cleavage structure has changed: national governments have started to become more and more reluctant to use their access to annulment proceedings to influence legal developments in many policy sectors as they no longer try to actively influence the legal dialogue in court.