Gee, John. "Formulas and Faith." Journal of the Book of Mormon and Other Restoration Scripture 21, no. 1 (2012): 60-65.

Gee, John. "A Tragedy of Errors." Review of Books on the Book of Mormon 4, no. 1 (1992): 93-119.

Gee, John. "Abracadabra, Isaac and Jacob." Review of Books on the Book of Mormon 7, no. 1 (1995): 19-84.

Gee, John. "Telling the Story of the Joseph Smith Papyri." FARMS Review of Books 8, no. 2 (1996): 46-59.

Gee, John. The Role of the Book of Abraham in the Restoration. Provo, UT: Foundation for Ancient Research and Mormon Studies, 1997.

Gee, John. A History of the Joseph Smith Papyri and Book of Abraham. Provo, UT: Foundation for Ancient Research and Mormon Studies, 1999.

Gee, John. The Ancient Owners of the Joseph Smith Papyri. Provo, UT: Foundation for Ancient Research and Mormon Studies, 1999.

Gee, John. "Facsimile 3 and Book of the Dead 125." In Astronomy, Papyrus, and Covenant, edited by John Gee and Brian M. Hauglid, 95-105. Provo, UT: Foundation for Ancient Research and Mormon Studies, Brigham Young University, 2005.

Gee, John, William J. Hamblin, and Daniel C. Peterson. ""And I Saw the Stars": The Book of Abraham and Ancient Geocentric Astronomy." In Astronomy, Papyrus, and Covenant, edited by John Gee and Brian M. Hauglid, 1-16. Provo, UT: Foundation for Ancient Research and Mormon Studies, Brigham Young University, 2005.

Astronomy, Papyrus, and Covenant In Studies in the Book of Abraham, Edited by John Gee and Brian M. Hauglid. Provo, UT: Foundation for Ancient Research and Mormon Studies, Brigham Young University, 2005.

Gee, John. Notes on the Sons of Horus. Provo, UT: FARMS, 1991.

Gee, John. "The Joseph Smith Papers Project Stumbles." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 33 (2019): 175-186.

Gee, John. "One Side of a Nonexistent Conversation." The FARMS Review 15, no. 1 (2003): 81-85.

Gee, John. "A Method for Studying the Facsimiles." The FARMS Review 19, no. 1 (2007): 347-353.

Gee, John. "New Light on the Joseph Smith Papyri." The FARMS Review 19, no. 2 (2007): 245-259.

Gee, John. "Some Puzzles from the Joseph Smith Papyri." The FARMS Review 20, no. 1 (2008): 113-137.

Gee, John. "Taking Stock." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 34 (2020): 113-118.

Gee, John. "Four Idolatrous Gods in the Book of Abraham." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 38 (2020): 133-152.

Gee, John. "Prolegomena to a Study of the Egyptian Alphabet Documents in the Joseph Smith Papers." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 42 (2021): 77-98.

Gee, John. "Fantasy and Reality in the Translation of the Book of Abraham." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 42 (2021): 127-170.

Gee, John. "Eyewitness, Hearsay, and Physical Evidence of the Joseph Smith Papyri." In The Disciple as Witness: Essays on Latter-day Saint History and Doctrine in Honor of Richard Lloyd Anderson, edited by Stephen D. Ricks, Donald W. Parry and Andrew H. Hedges, 175-217. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2000.

Gee, John. "The Role of the Book of Abraham in Latter-day Saint Scripture." In A Guide to the Joseph Smith Papyri, 42-45. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2000.

Gee, John. "Theories to Explain the Book of Abraham." In A Guide to the Joseph Smith Papyri, 18-31. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2000.

Gee, John. "Historical Overview." In A Guide to the Joseph Smith Papyri, 1-13. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2000.

Gee, John. A Guide to the Joseph Smith Papyri. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2000.

Gee, John. "Selling Our Birthright for a Mess of Pottage: The Historical Authenticity of the Book of Abraham." In 2018 FairMormon Conference. Provo, UT: FAIR, 2018.