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

Gee, John. "Has Olishem Been Discovered?" Journal of the Book of Mormon and Other Restoration Scripture 22, no. 2 (2013): 104-107.

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

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

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

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

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. "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.

Gee, John. "Verbal Punctuation in the Book of Mormon I: (And) Now." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 50 (2022): 33-50.

Gee, John. "Verbal Punctuation in the Book of Mormon II — Nevertheless." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 57 (2023): 195-206.