The article considers the features of archival institutions of the Moscow region in the period of their occurrence in structure of the organs of the NKVD (from 1939 to 1946). Novelty of research consists in the absence of scientific works, reflecting the work of archival institutions of the region during the considered period; in works on the history of archives in the Soviet Union the problems reflected in fragments. The involvement of the archival and other sources that were never used before raises its value on the historical side and promotes further continuation of research work in this direction: study of the dual role of subordination of all parts of the archival institutions to the bodies of internal Affairs, when many archival documents were classified, reduced their use in print and scientific purposes, however, ensuring safety of archives and social security of their employees improved. The establishment in March 1941 off the State archive Fund of the USSR, which to a great extent contributed to the centralization of archival Affairs, the subordination of the archival institutions of power office allowed to carry in shortest terms a grandiose work of evacuation of the vast array of archival documents on the East of the country. Enormous damage caused to the archival service of Moscow region during the war, restoration work on the territory of Moscow region in the years of The Great Patriotic War of archival institutions, can be regarded as independent research theme. This article shows the merit of individual employees of the archival service of the Moscow region during the considered period, primarily chief of Department of state archives administration of the Management NKVD of Moscow region A.N. Gavrilov, his deputy V.E. Derbin, head of the Archive of the October revolution and socialist construction of the Moscow region, M.I. Artamonova and others. In the article reflects one of the most difficult stages of the development of archival Affairs on the territory of the Moscow region. The main task was saving from the death of the documents of the State archival Fund of the USSR, which was done by the prince of the great effort of the archivists and organizational coherence of the state mechanism.