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The Josephus Stuart papers contain correspondence, diaries, and documents related to Stuart's early medical practice and his service with the 29th regiment of the United States Infantry. The collection also includes a series of diaries written by Stuart between 1815 and 1821, which document Stuart's service as chancellor to the U.S. Consulate in London, a visit to former president Thomas Jefferson at Monticello in 1816, and Stuart's experiences operating a steamboat.

The Josephus Stuart collection contains 34 letters, dated 1810-1834, the majority of which belonged to Stuart, though six letters are addressed to Gerrit Wendell, a Washington county judge and former member of the New York state senate. In addition, the collection contains 38 documents, nine of which are associated with Stuart's father-in-law, Enoch Leonard. Several of the papers deal with Stuart's early medical practice, including a letter regarding research related to Stuart's medical thesis, which was a defense of cutaneous absorption. Other documents concern Stuart's military service with the 29th regiment, United States Infantry, including his commission as paymaster, signed by President James Madison.

Of primary significance are Stuart's eight diaries, written from 1815 to 1821. The early diaries document Stuart's period as chancellor to the U.S. Consulate in London. He records the sea voyage, as well his observations of English life and customs, often unfavorably comparing them with his views on conditions in America. The diaries also record trips Stuart took to Ireland, Scotland, France, and the Netherlands; he took care to note his observations during his travels, including the landscape, sights, lifestyle, living conditions, economy, and politics. Diaries four and five recount Stuart's return to the United States and include a detailed account of his visit with Thomas Jefferson at Monticello on December 24 and 25, 1816. He recorded Jefferson's views on a wide variety of topics, and made notes on his appearance and home. Also contained within diary five are accounts of Stuart's role as agent for Francis Cazeau, James Monroe's inauguration, travels to Ohio, encounters with Native Americans, and various business transactions, including his steamboat venture. The next several diaries record his experiences running the Walk-in-the-Water, his marriage to Ann Leonard in May 1818, and the beginning of his financial troubles in 1819. In the last diary (#8), Stuart had settled in Jamesville, New York, as an attorney. The last month of the diary records the loss of the steamboat, which ran aground during a gale in 1821.

Also included in the collection are a set of architectural plans by noted New York architect Philip Hooker. Hooker designed a house for Stuart in 1818, which was apparently never built; the plans are contained within a small booklet. The Stuart papers also have eleven items related to family genealogy, and three 1810 New York newspapers.