The article fills an important gap in the history of Russian (Soviet) physical anthropology. Based on previously secret archival papers discovered by the author, the history of anthropological research in prisoner-of-war camps on the territory of the USSR in the 1940s is revealed. Following the example of anthropologists during World War I, Soviet anthropologists, led by Viktor Bunak, initiated and carried out an extensive research program under the auspices of the Presidium of the USSR Academy of Sciences in close cooperation with the NKVD authorities. The published archival materials strictly document the work of the scientists, who in 1943 proposed the idea of this large-scale study, and presented the project to the Deputy Chairman of the Council of People’s Commissars, Andrey Vyshinsky. The immediate permission to conduct the expedition was personally given by Lavrentiy Beria. The project was carried out in 1944–1946 under strict secrecy, which also was extended to the publication of its results. Specific information is provided on the conduct of anthropological research in a number of prisoner-of-war camps, the composition of the expedition, instructions, and methodologies. The article analyzes the reasons why the entire history and results of this project remained classified as secret until the collapse of the USSR. The article is preceded by a review of anthropological research by Russian (Soviet) scientists involving special contingents as informants, explaining why special contingents (army conscripts, military personnel, mentally ill individuals, prisoners in prisons and camps) were actively used in anthropological research.