The purpose of this article is the analyses of discussion between Albert Einstein and Werner Heisenberg in the period 1925-1927. Their disputes, relating to the sources of scientific knowledge, its methods and the value of knowledge acquired in this way, are part of the characteristic for the European science discourse between rationalism and empirism. On the basis of some sources and literature on the subject, the epistemological positions of both scholars in the period were reconstructed. This episode, yet poorly known, is a unique example of scientific disputes, whose range covers a broad spectrum of methodological problems associated with the historical development of science. The conducted analysis sheds some light on the source of popularity of logical empirism in the first half of the 20th century. A particular emphasis is placed on the impact of the neopositivist ideas which reflect Heisenberg's research program, being the starting point for the Copenhagen interpretation of quantum mechanics. The main assumption of logical empirism, concerning acquisition of scientific knowledge only by means of empirical procedures and logical analysis of the language of science, in view of the voiced by Einstein arguments, bears little relationship with actual testing practices in the historical aspect of the development of science. The criticism of Heisenberg's program, carried out by Einstein, provided arguments for the main critics of the neopositivist ideal and contributed to the bankruptcy of the idea of logical empirism, thereby starting a period of critical rationalism prosperity, arising from criticism of neopositivism and alluding to Einstein's ideas.