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Václav Černík (1931 – 2017) was one of the founders of modern philosophy of science in Slovakia. This paper focuses on his lifelong project of founding a Marxist methodology of science based on a reconstruction of Marx’s Capital. The project had three main pillars: (1) a theory of a new type of scientific law, (2) dialectics as a theory of philosophical categories, and (3) a historical account of types of rationality. In the paper, we contextualize the various stages of the project: from Černík’s early works on scientific laws and thought experiments to his attempt at constructing a system of categories, as well as publications in methodology after 1989. Our critical assessment shows that Černík was the first to deal with certain topics in the Slovak context. His approach also had certain advantages vis-à-vis with other attempts at the time, especially due to the author’s open-minded attitude to modern logic and Western philosophy of science. On the other hand, the project was never finished and it left a number of characteristic problems unsolved (e.g., the nature of dialectical contradictions, difficulties with using logical instruments to formulate philosophical intuitions).