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In our report, we perform an epistemological analysis of thought experiments. We consider the historical background of this research tool, its specificity, distinctive features of its functioning either in the system of natural sciences and in the economic theory. We analyse the nature of the relationship between a material experimentation and a thought experiment and the status of results of each of these procedures to acquire new knowledge. We claim that thought experiments in the economic theory and in natural sciences are fundamentally different and that the isolated thought experiment is not a full value research tool for investigating the reality but a good mean for mapping and structuring the subject area.