As higher education in the United States has changed over the last 20 years, agencies responsible for quality assurance have had to adapt both their standards and processes. More recently, calls for greater accountability of the higher education sector have led to new challenges for quality assurance agencies, with respect to their role, purpose, standards and processes. This paper will review the challenges brought about by changes to higher education, and how accrediting agencies and others have responded with major reforms and initiatives. While these have had significant effect, they may not be sufficient to address the most recent calls for higher education and accreditation to address in very specific ways five key issues: improving retention and graduation rates; identifying learning outcomes for degrees and setting higher standards of student learning; providing greater transparency about the outcomes of both higher education and accreditation actions; responding to innovation, especially distance education; and most recently, addressing abuses in the for-profit sector. Each of these areas will be explored along with the challenges they present to the current system of quality assurance through accreditation.