In an effort to ensure accountability, and in order to prepare students for a globalised world, the higher education sector in Mexico is seeking to implement an evaluation of public higher education. Higher education institutions (HEIs) need to balance this goal against the need to protect their autonomy. This would be preserved if each institution were to operate an efficient evaluation system which is designed and executed, at least in part, by the institution itself. The process must be effective and transparent, allowing a clear communication flow to be built up with the general public as well as with the educational authorities. HEIs must, therefore, rethink an earlier conception which presupposes that maintaining the quality and good functioning of education is a purely internal affair. Implementing evaluation systems at national level is relatively new, so it is still experiencing some problems in relation to co-ordination as well as resistance from evaluees.