The study of scientific book publishing, due to its enormous social and state significance, is an urgent task of modern research. This article is the first to consider the system of scientific book publishing in the Siberian Branch of the Russian Academy of Sciences (SB RAS) in the period of 2001–2010 thus determining and adding to the history of regional and Russian scientific book publishing. The purpose of the study is to present the development of the system for publishing scientific literature in the SB RAS during this period. The source base of the study is representative: these are numerous documents of the current archives of the Siberian enterprise “Nauka” RAS (Novosibirsk Printing House No. 4) and the Siberian Publishing Company “Nauka” RAS, regulatory acts of the Presidium of SB RAS, Annotated thematic plans for the release of scientific literature for 2002-2010, Publishing houses of SB RAS, materials of the weekly newspaper SB RAS “Science in Siberia” for the same period.The revealed data allow reconstructing the picture of the scientific book publishing system development in SB RAS and its thematic orientation in the first decade of the XXI century. The results obtained show that the prevailing part of published scientific literature – every third edition – during this period was on archeology, history, philology, philosophy, law.The study refined quantitative data on the release of serial publications, revealed the role of the Presidium SB RAS in developing the system of scientific book publishing, expanded the idea of cooperation between SB RAS and SIF “Nauka” RAS.The results obtained provide an opportunity to redefine and assess the evolution of their relationship during the period under review. The continuing decrease in the share of CIF in the total volume of publications of SB RAS can be interpreted as the crisis increase, but the implementation of significant and complex publishing projects speaks for a new paradigm of relations between them: mutually beneficial, effective and promising.