Jointly with Prof. Klaus Marxen (Humboldt University of Berlin), Prof. Werle supervised the research project "Criminal Justice and the GDR past".  Since 1996, all criminal proceedings of crimes concerning the GDR regime had been evaluated in the context of the project, funded by the Volkswagen Foudation and the Federal Foundation for the Reappraisal of the SED Dictatorship. The outcome of the project was, in addition to several dissertations, a seven-volume documentary series complemented by a résumé volume (Marxen/Werle, Die strafrechtliche Aufarbeitung von DDR-Unrecht - Eine Bilanz) and a brochure with statistical data (Marxen/Werle/Schäfter, Die Strafverfolgung von DDR-Unrecht - Fakten und Zahlen).