Thomas Jefferson’s papers did not remain in an intact collection after his death; they are now located in more than 900 different repositories all over the world. Several different editions of his papers have been published since his death, but none of them are comprehensive or complete so far. This guide will help you navigate the different sources of Jefferson documents to locate the information you need.
...the document can be located in the Papers of Thomas Jefferson section of Founders Online. You can browse by date or correspondent, or search for specific keywords. Note that this database includes transcriptions that have not been fully verified by the Papers of Thomas Jefferson and Papers of Thomas Jefferson: Retirement Series staff; these are "early access" documents.
Note that the currently available letterpress editions of the Papers of Thomas Jefferson and Papers of Thomas Jefferson: Retirement Series provide access to a slightly different set of documents:
Papers of Thomas Jefferson: 1760 through 10 March 1804 (42 volumes)
Papers of Thomas Jefferson: Retirement Series: March 1809 through January 1819 (13 volumes)
There is one small gaps which is not covered by either Founders Online or the current letterpress volumes: 11 March 1804 through 30 June 1804
If you are looking for a document from that time period, you have a few options:
If you are at Monticello, you can use the Papers of Thomas Jefferson control cards (available on microfilm at the Jefferson Library) to ascertain the location of the document, then either consult the relevant microfilm of the document here or contact the owning repository.
Check the Thomas Jefferson: Papers collection in Hathi Trust, which contains the full text of all the major published editions of Jefferson's writings, including the Washington, Ford, and Lipscomb-Bergh editions. (Note that these editions do not include incoming correspondence.)
Check the Thomas Jefferson Papers collection at the Library of Congress. A relatively high proportion of documents from Jefferson's presidency are located at the Library of Congress. Note that the search engine only searches the headings for documents (usually just the names of the correspondents and the dates), and the text of the transcription if the Library of Congress has included it. Only some of the documents have accompanying transcriptions.
Other significant online sources of transcribed Jefferson documents are the Founder's Constitution website (check the author index for a list of Jefferson documents) and the From Revolution to Reconstruction collection, hosted by the University of Groningen. It also sometimes fruitful to simply search Google, and especially Google Books, for the document you are looking for, as many individual documents have been published in other books and articles.
Finding Documents on a Specific Topic
If you are searching for documents on a certain topic, or that concern a specific person, the best strategy is to first consult sources which will allow you to search as many documents as quickly as possible.
Check Papers of Thomas Jefferson and Papers of Thomas Jefferson: Retirement Series, using either the fee-based or free online version. If you must resort to the print edition, Volume 21 is a cumulative index for the first 20 volumes. The indexes for all published PTJ:RS volumes can be searched here on the Monticello website.
There is no way to comprehensively search all documents for the periods not covered by Princeton yet. The best you can do is search the Thomas Jefferson: Papers collection in Hathi Trust, which contains the full text of all the major published editions of Jefferson's writings, including the Washington, Ford, and Lipscomb-Bergh editions.
There are a number of smaller editions of Jefferson papers, usually highly specialized by topic, which may contain a document you are looking for. You may wish to consult any or all of these, depending on your research topic:
Betts, Edwin M., and James Bear, Jr., eds. Family Letters of Thomas Jefferson. Columbia, MO: University of Missouri Press, 1966. Reprinted Charlottesville: Thomas Jefferson Memorial Foundation, 1986. This volume contains selected correspondence between Thomas Jefferson and his children, grandchildren, siblings and in-laws.
Cappon, Lester J., ed. The Adams-Jefferson Letters. Chapel Hill NC: University of North Carolina Press, 1959. Rep. 1988. This two-volume work contains the complete correspondence between Thomas Jefferson and John Adams, spanning the years 1777-1826. It also includes letters to and from Abigail Adams.
Lastly, it is often worthwhile to simply search Google and especially Google Books for the letter or reference you are looking for. This may yield a useful citation to a published edition of Jefferson's writings, or sometimes a one-off transcription of the document.