The diaries and photographs of the missions, as well as the botanical specimens, are stored together at the Ryukoku University Library. The Otani Collections are now located in Japan, China and Korea:
- The Omiya Library at Ryukoku University, Japan
- The Tokyo National Museum, Japan
- The Kyoto National Museum, Japan
- The Lüshun Museum, China
- The National Museum of China
- The National Library of China
- The National Museum of Korea
A further portion of the materials from Otani’s missions were sold to private collectors, and their location is now unknown.
The Otani collections include Chinese Buddhist sutras from Dunhuang and other sites including Turfan. The collections also include manuscripts in other languages including Buddhist sutras written in Sanskrit using the Brahmi script, Buddhist sutras and Manichaean documents in Sogdian, Tibetan, Tangut and Uyghur. These were found along the northern Silk Road in Kucha and the tombs of Astana and Gaochang.
