Gee, John. "Limhi in the Library." Journal of Book of Mormon Studies 1, no. 1 (1992): 54-66.

Gee, John. "“Bird Island” Revisited, or the Book of Mormon through Pyramidal Kabbalistic Glasses." Review of Books on the Book of Mormon 7, no. 1 (1995): 219-228.

Gee, John. "A Seething Pot in the North: International Affairs Leading Up to Lehi's Day." In Glimpses of Lehi's Jerusalem, edited by John W. Welch, David Rolph Seely and Jo Ann H. Seely, 543-560. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2004.

Gee, John. "A Seething Pot in the North: International Affairs Leading Up to Lehi's Day." In Glimpses of Lehi's Jerusalem, edited by John W. Welch, David Rolph Seely and Jo Ann H. Seely, 543-560. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2004.

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

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. "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.