In this paper, we review the current official methodology of scientific research output evaluation in the Czech Republic and present a case study on twenty-one Czech public universities. We analyze the results of four successive official research assessment reports from 2008 to 2011 and draw the following main conclusions: (a) the overall research production of the universities more than doubled in the period under investigation, with virtually all universities increasing their absolute research output each year, (b) the total research production growth is slowing down and (c) Charles University in Prague is still the top research university in the Czech Republic in both absolute and relative terms, but its relative share in the total research performance is decreasing in favor of some smaller universities. We also show that the rankings of universities based on the current methodology are quite strongly correlated with established indicators of scientific productivity. This is the first time ever that the official present-day Czech science policy and evaluation methodology along with the results for the Czech university system has been communicated to the international public.
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