There have been calls to increase the autonomy of higher education institutions in Europe for a number of years. They have been counterbalanced by demands for increasing accountability and a European quality assurance system. In London in 2007, the European ministers of education decided to implement a European register of accredited quality agencies, and defined standards for registration. Being part of the register requires "substantial compliance with all standards" instead of "full-compliance". This might take into consideration the context of the national higher education system, the role of the agency in the quality assurance system, and even the national culture and traditions, allowing for different interpretations, some imprecision, and diverse degrees of flexibility and compliance. Indications from the United States suggest an emerging desire at the federal level to play a more visible role in regulating higher education through intervention in the accreditation system to ensure increased institutional accountability. This may have a parallel in the European situation. While in the United States the attempts at increased federal control have so far apparently failed, in Europe quality systems linked to higher education institutions were replaced with "independent" accrediting agencies. We analyse these changes and offer a possible interpretation for the differences on the two sides of the Atlantic.