Jada Pinkett-Smith had auditioned to play Trinity, but said in an interview that she and Reeves had no chemistry even though they would later become friends. In the sequel, Pinkett-Smith would play the character Niobe.

Although meant to look like computer code, the symbols are actually a combination of reversed characters and numbers that the visual effects supervisor scanned from his wife's Japanese cookbooks.

Born Thomas A Anderson, his computer programmer/hacker name "Neo" is an anagram for "The One".

A copy of Neo's passport is seen by Agent Smith, with the expiration date of September 11, 2001. 2 1/2 years after the film's release, New York's Twin Towers would be destroyed by a terrorist attack on that exact date.

As described by Morpheus: "You take the blue pill ... the story ends. You wake up in your bed and believe whatever you want to believe. You take the red pill ... you stay in Wonderland, and I show you how deep the rabbit hole goes." Of course, Neo chooses the red pill and joins the rebellion.

The Nebuchadnezzar is named for Nebuchadnezzar II, an ancient Babylonian king who was said to have troubling dreams he couldn't remember. In Matrix Reloaded, Morpheus quotes the Bible as the Nebuchadnezzar is destroyed: "I have dreamed a dream; but now that dream is gone from me."

Mouse claims credit for the Woman in Red, a simulated character in the Agent training program. Meant to appear harmless, she catches the trainee's attention by wearing a vibrant shade of red and smiling flirtatiously. She then transforms into an armed Agent, with the lesson that any "bluepill" can be overwritten by an Agent in the Matrix.

Sets from Dark City (1998), including rooftops, buildings, and other exterior sets, were used in The Matrix. The rooftops that Trinity runs across at the beginning of the film are the same ones that John Murdoch runs across in Dark City.

Although Neo's "virtual reality" life is in 1999, the Resistance calculates the current year of the Real World to be approximately 2199.

As gatekeepers of the Matrix, Agents are sentient computer programs that can move in and out of any software hardwired to the Matrix, including the imprisoned human's avatars, or virtual bodies.