This article examines challenges for accountability arising from the development of the Schengen law within the framework of the European Union. Building upon the substantive body of research by other authors on general implications of the integration of the Schengen acquis, it focuses on recent developments after the entry into force of the Treaty of Amsterdam and evaluates to what extent the European institutions have so far met the challenges for accountability stemming from the intergovernmental origin of the Schengen law. The article identifies various persisting deficiencies in the areas of transparency, institutional balance and judicial review and proposes specific actions, which should be addressed vigorously by the European institutions.