Gee, John. "Four Suggestions on the Origin of the Name Nephi." In Pressing Forward with the Book of Mormon: The FARMS Updates of the 1990s, edited by John W. Welch and Melvin J. Thorne, 1-5. Provo, UT: FARMS, 1999.

Gee, John. "Two Notes on Egyptian Script." In Pressing Forward with the Book of Mormon: The FARMS Updates of the 1990s, edited by John W. Welch and Melvin J. Thorne, 244-247. Provo, UT: FARMS, 1999.

Gee, John. "Notes and Communications: Two Notes on Egyptian Script." Journal of Book of Mormon Studies 5, no. 1 (1996): 162-176.

Gee, John. "Notes and Communications: New and Old Light on Shawabtis from Mesoamerica." Journal of Book of Mormon Studies 6, no. 1 (1997): 64-69.

Gee, John. "Epigraphic Considerations on Janne Sjodahl’s Experiment with Nephite Writing." Journal of Book of Mormon Studies 10, no. 1 (2001): 25, 79.

Gee, John. "Daniel H. Ludlow, ed., The Encyclopedia of Mormonism." Review of Books on the Book of Mormon 5, no. 1 (1993): 172-182.

Gee, John. "The Grace of Christ." FARMS Review 22, no. 1 (2010): 247-259.

Gee, John. "Who Was Not the Pharaoh of the Exodus." FARMS Review of Books 9, no. 1 (1997): 43-50.

Gee, John. "Egyptian Society during the Twenty-sixth Dynasty." In Glimpses of Lehi's Jerusalem, edited by John W. Welch, David Rolph Seely and Jo Ann H. Seely, 277-298. Provo, UT: Foundation for Ancient Research And Mormon Studies, 2004.

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. The Crocodile God of Pharaoh in Mesopotamia In Insights. Vol. 108. Foundation for Ancient Research and Mormon Studies, 1996.

Gee, John. "The Wrong Type of Book." In Echoes and Evidences of the Book of Mormon, edited by Donald W. Parry, Daniel C. Peterson and John W. Welch, 307-329. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2002.

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. "“An Obstacle to Deeper Understanding”." FARMS Review of Books 12, no. 2 (2000): 185-224.

Gee, John. "On Corrupting the Youth." The FARMS Review 22, no. 2 (2010): 195-228.

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. "The Corruption of Scripture in Early Christianity." In Early Christians in Disarray: Contemporary LDS Perspectives on the Christian Apostasy, edited by Noel B. Reynolds, 163-204. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2005.