Valve co-founder Gabe Newell is credited in the game as an additional tester. More information on his involvement can be found in an extensive write-up by director and producer Warren Spector published by Gamasutra a few months after the game's release in 2000. Newell was the first of several industry friends (including developers from Looking Glass Studios and Irrational Games after him) to play-test and criticize the prototype missions they had ready in mid-1999, with Spector noting he "correctly identified the utter lack of tension" in the game's skill and augmentation systems, forcing them to completely change their design approach, with lead designer Harvey Smith revising them significantly for the final game.

A Linux port was in development by Loki Software, however the port was cancelled due to Loki Software ceasing operations.

In the Japanese release of Deus Ex, several minor changes were made that altered the game's menu/text presentation and moreso made the gameplay generally easier:
• The Power Recirculator will increase the power drain rate of augmentations.
• Player-owned weapons will do x4 damage to enemies and level obstacles like doors on Easy difficulty.
• All damage taken has a passive 40% reduction.
• The "Dragon's Tooth" sword deals 50 damage instead of 20.
• Note adding, editing, and deleting is disabled.
• Normal text color is changed from 0,255,255 to 255,255,255.
• Player text color is changed from 255,255,255 to 128,255,255.
• All English fonts in text and item selection are replaced with Japanese fonts and names for items respectively
• Infolink text slowed from 1 character per 0.03 seconds to per 0.09 seconds.
• The version string in the main menu is removed.

In the Hell's Kitchen sewer lab where the player has to rescue the smuggler's friend Ford Schick, there is a computer which can be hacked to find an e-mail regarding a company picnic. The e-mail is signed by a woman named "Harleen Quinzell", the real name of Batman's Harley Quinn. Her signature also includes the line, "A frown is just a smile turned upside down...", a line that would be fitting for the same character.

One of the e-mails on Paul Denton's computer in the 'Ton Hotel mentions the movies "Blue Harvest" and "See You Next Wednesday." "Blue Harvest" was the original working title of the Movie Star Wars Episode VI: Return of the Jedi and "See You Next Wednesday" is a commonly used line in John Landis films.

Hidden in the game are a number of excerpts from real books. Among these books are "The Man Who was Thursday" by G.K. Chesterton (whose plot coincides with the plot of the game) and "The Eye of Argon " by Jim Thies (considered to be the worst Sci-fi genre book of all time).

According to Designer Harvey Smith, J.C. Denton is a descendant of Jesus Christ.

Deus Ex was released on June 26, 2000, over a year before the September 11th attacks, but has sections of the game where New York City's skyline is visible, and the Twin Towers of the World Trade Center are missing. According to lead game designer Harvey Smith in a 2003 interview promoting Deus Ex: Invisible War, the Twin Towers existed in the game's files as separate textures, but he claimed they were left out due to the game's texture memory being too high (the combined New York City skyline textures equal 11 kilobytes):


The game itself makes no mention of the Twin Towers being destroyed by terrorists. Years later in 2012, creator Warren Spector gave a slightly different account of how they went missing: