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In this article, 93 Greek university departments were evaluated according to their academics' h-index. A representative sample from the fields of social sciences and humanities, sciences, engineering, pharmacy and economics was adopted. In the reported study, 3354 (approximately 1 out of 3) academics serving in Greek universities were evaluated. The number of papers, citations and h-index have been collected for each academic, department, school and university using the Google Scholar scientific database and the citations analysis software program Publish or Perish. Analysis revealed that departments of the same academic discipline but located in different universities are characterised by strong differences on the scientific outcome. In addition, in the majority of the evaluated departments, a significant difference in h-index was observed between academics who report scientific activity on the departments' website and those who do not. The viability of the adopted method for measuring and ranking the scientific performance of higher education departments proved to be quite high. (Contains 19 tables.)