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. 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. "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 Keeper of the Gate." In The Temple in Time and Eternity, edited by Donald W. Parry and Stephen D. Ricks, 233-273. Provo, UT: Foundation for Ancient Research and Mormon Studies, Brigham Young University, 1999.