Purpose. The history of the study of the Neolithic site with flat-bottomed ceramics of the Trans-Urals and Western Siberia is considered. Until the end of the 20th Century, such complexes in the region were correlated with the Boborykino culture. The formation of ideas about the main components of this culture determined the essence of the first two stages of the study of culture (from 1961 to the first decade of the 20th Century). Results. At the first stage, in the publications of K. V. Salnikov and L. Ya. Krizhevskaya, the characteristic features of the newly identified culture are defined: flat-bottomed ceramics with original ornaments and the microlithic character of flint inventory; the chronological positions of the culture are determined by the Eneolithic – Early Bronze Age. At the second stage, in the publications of V. T. Kovaleva and her colleagues, the Boborykino culture is assigned to the second stage of the development of ceramic ornamental traditions of the Neolithic Trans-Urals. The culture dates from the third quarter of the 6th – the first quarter of the 4th millennium BC. Initially, the autochthonous line of development of this culture from the early Neolithic Koshkino culture was substantiated. However later the alien character of this culture as a result of migration in the Trans-Urals of the early agricultural population of the Near East and the Caucasus began to be declared. At the third stage, by researching new archaeological sites in the Baraba forest-steppe and Middle Ob region, the age of archaeological sites with flat-bottomed ceramics was raised to the 7th – 6th millennium BC; the difference between local ceramics and Boborykino complexes was shown. The comprehension of sites with flat-bottomed ceramics of the period 7th – 6th millennium BC began as a new independent cultural-chronological phenomenon in the Neolithic of the Trans-Urals and Western Siberia. Conclusion. A version of the autochthonous origin of the Baraba culture is expressed. However, migration theories of the appearance of such archaeological sites in the north of Eurasia in their variations can also be discussed.