The Illuminatus! Trilogy is a novel by Robert Anton Wilson and Robert Shea, confirmed by Damon Lindelof  as an influence on Lost. It is a Discordian conspiracy theory novel, with several themes in common with the show; the number 23 is also heavily involved in the trilogy.
- One of the many intertwined plots of The Illuminatus! Trilogy is about a synthesized virus, Anthrax Leprosy Mu, which is one option in an Illuminati plan to kill off large amounts of humanity. This draws parallels to Mittelwerk's plot as revealed by the Sri Lanka Video.
- The "lost continents" of Atlantis and Mu are heavily involved in the trilogy, mysterious islands with an ancient mythology element.
- One of the heroes is named Joe Malik.
- In Jughead, Juliet refers to Latin as being for "the enlightened." This may be a synonym for the Illuminati.
- In the Illuminatus! Trilogy, the Lovecraftian entity Yog Sothoth is help captive inside the Pentagon by the pentagon shape itself. Toward the end of the novel the Pentagon is partially destroyed, and a member of the Illuminati is killed by Yog Sothoth while attempting to fill in the blasted part of the pentagon with chalk. This draws parallels to the ash circles used to keep out the Monster.