This paper studies the accounting system reform practised in Greek universities since January 2000, and more particularly at the Aristotle University of Thessaloniki (AUTH). It specifically examines the allocation of resources to faculties by university management based on certain criteria. The AUTH is the largest public university in Greece and one of the largest in Europe. Following a study of financial data on variances in expenditure over the past 12 years, the application of a new method for allocating funds to departments is proposed through use of a certain formula. The results from the application of the formula for resource allocation have shown that the latter needs to be modified in order to be considered fairer and be accepted by the academic community. (Contains 3 tables.)