The use made of evaluation output is crucial for understanding the position and effectiveness of evaluation systems. This article examines the development of evaluation in the Italian university system from the 1990 s onwards where serious problems have been and continue to be addressed in the use of evaluation output to improve academic activities and make universities accountable for their behaviour. There is a tendency for evaluation to generate inappropriate or undesired effects and for those being assessed to adopt opportunistic behaviour. Underestimation of the universities’ organisational features is the main reason for so many difficulties.