In this article, we present a comparative analysis of the organization of public funding of research in three central and eastern European countries. We first compare the organization of funding agencies, the portfolio of funding instruments and, finally, the repartition of funding by beneficiaries. Further, we identify the main structural characteristics of the funding systems, by looking at features like sectoral divisions, level of delegation and the role of different institutional levels in the management of funding. Against a widespread conception of research policies in central and eastern European countries converging towards a western-style model, our study displays profound differences between the considered countries, related to history but also to contextual factors in the reform phase.