The Tokyo Imperial Household Museum bird collection held by the Yamashina Institute for Ornithology (YIO) contains many specimens originated from the United States National Museum (USNM) at the Smithsonian Institution. Although the collection includes specimens of extinct species and type specimens, the specimen information kept in the YIO is incomplete. We examined various materials such as ledgers related to the specimens from USNM to clarify the collection transfer history. Our examinations indicated that the specimens from USNM in the Tokyo Imperial Household Museum collection had been derived via three routes: USNM sent (1) 431 specimens to the present Tokyo National Museum in 1877, (2) 773 specimens to the present National Museum of Nature and Science, Tokyo (NSMT) in 1877, and (3) 117 specimens to the present NSMT in 1887. We also confirmed that almost all the specimens from USNM are remained in YIO. The present study demonstrates that ledgers and notes on specimens are useful to clarify the collection transfer history which may improve the incomplete collection data.