Japanese universities are currently experiencing rapid development in quality assessment and assurance activities. In 2004, the national government introduced corporate-style governance into national universities, accompanied by a new evaluation scheme to be carried out by both a governmental committee and a national agency called the National Institution for Academic Degrees and University Evaluation. Most local public universities operated by prefectures and cities have also adopted corporate-style governance and face pressure from local assemblies to engage in formal performance assessment. Furthermore, since 2004 the Japanese government has required seven-year, cyclical 'certified evaluations' (accreditation) for all national, local public and private universities and colleges. This certified evaluation is implemented at the institutional level and applies to new and evolving forms of professional post-graduate education programmes. Project-based funding schemes, such as 'Centres of Excellence (COEs)' in research and 'Good Practices' in various other education programmes are regarded as indirect forms of performance assessment. Despite the implementation of these initiatives, however, the means by which the quality of university education and research is best assessed remains the subject of hot debate, especially within the humanities and social sciences. This article considers the latest initiatives in quality assessment and assurance of education and research activities in Japan, focusing on policy and administrative reform and the particular challenges faced by the social sciences.