The practice of carrying out systematic research evaluations between the state and institutions of higher education can be characterised as fragmented in Germany. This has a lot to do with the multi-layered character of the system. The German scientific landscape is one of the largest and most diverse in Europe, but it also encompasses a multitude of actors, each with different interests and procedures for evaluation. Indeed, the fragmented character of Germany’s higher education system is likely to become further pronounced under Federal reforms of the present government. A forerunner in the field of research evaluation in higher education is the Academic and Research Commission of the state of Lower Saxony. As this body has been active since 1999, its organisation and procedures will be presented as a case study for possible developments and the impact of such procedures in the German scientific system. The article closes with considerations on future prospects of systematic research evaluations in Lower Saxony and in Germany.