In this paper we outline how large German research universities handle the Bologna reform. We in particular describe how they fulfill the requirement to accredit their new undergraduate and graduate programs. A description of the general framework is complemented by specific examples and experiences gained in the accreditation process of the computer science programs at the University of Freiburg. We in particular illustrate the positive effects of peer review in the accreditation process for the design and implementation of the new degree programs and disclose hurdles solved for the accreditation. It turns out that the external program accreditation of all degree programs is complex and expensive. Therefore, large traditional universities go for the so called systems accreditation. The aim is to make external program accreditation superfluous once an efficient internal quality management system is implemented and operational. We outline some advantages and disadvantages of system accreditation (Systemakkreditierung) versus program accreditation and conclude with lessons learned during our accreditation experience.