Duke has focused its collecting on 19th and 20th century Japan, identifying a few areas of strength - modern art history, women's and labor history, Japan's colonial history, modern literature, manga and anime.  Some of these - such as labor history - date from the earliest hires in Japanese studies, while others are quite recent, although efforts have been made to build the collection retrospectively, especially in modern art history.  Rather than trying to build a comprehensive collection, the primary aim is to support the faculty and students in the Triangle and to a lesser extent, to be a regional resource for faculty in the Southeast. The primary focus is on history, literature and the social sciences from 1868 to the present, but premodern social and economic history, and Buddhism are well represented, and basic materials are collected in premodern literature, religion, philosophy, language, law, sociology and anthropology. The collection also contains works in Japanese on Chinese art history, Daoism, Chinese and Korean history in the nineteenth and twentieth centuries, the Japanese colonial experience, US-Japan relations, the history of the European Community, world history and translations of world literature into Japanese.

Research that crosses both disciplinary and national boundaries is expanding the boundaries of the collection. This has meant that primary importance has been given to reference tools, electronic and print, that facilitate the identification of resources and core titles as well as materials directly relevant to faculty and graduate student research.  The abundance of reprints being published in Japan has allowed Duke to acquire primary sources, especially visual ones.  With the advancement of digital technology, the globalization of culture, and the breakdown of traditional knowledge, interdisciplinary and transcultural approaches to visual studies are imperative in the teaching and research of Japan. And given the programmatic emphasis on popular culture, Duke has built significant collections in advertising,  film, women's magazines, manga and anime.

Duke's Rubenstein Library has a strong collection of reports from missionaries, early British diplomats to Japan, the East India company papers, diaries and letters from merchants and seamen as well as items in such collections as the Stereographic card collection, 1860-1928, and the postcard collection.  For Japan, it also has the Papers of General Robert L. Eichelberger (1886-1961), who commanded all ground occupation troops in Japan (1945-1948), and materials related to Japanese advertising in the Hartman Center.   There are also smaller collections such as Japanese wartime propaganda publications.