Because of her role in The Queen (2006), Helen Mirren was invited to meet Queen Elizabeth II, but couldn't make the meeting because she was in South Dakota filming this movie.
Director of photography Amir M. Mokri was replaced by John Schwartzman several months into shooting. This was reportedly due to "creative differences" between Mokri and director Jon Turteltaub.
The name on a realty sign in the background of one of the scenes is Segars' Realty. A reference to one of the film's executive producers Charles Segars.
Release prints were delivered to theaters with the fake title 'Cinnamon'.
Patrick Gates makes a reference to FDR during World War Two. Jon Voight played Franklin Delano Roosevelt in Pearl Harbor (2001).
For the theatrical release, the film was called "National Treasure: Book of Secrets," but for the DVD release, the title was changed to "National Treasure 2: Book of Secrets."
In the Booth diary the remaining part of the page after the words Thomas Gates Artifex (artifex: Latin) adj., skilled, masterful) is the word Aenigmatum, or enigma. The two Latin words brought together mean one who is skilled in puzzles.
As stated in the commentary, experts were brought in to match President Lincoln, Queen Victoria and President Coolidge's handwriting.
The script originally called for Mitch Wilkinson to stab Patrick Gates in the scene where they escape from the flooding gold city. This was taken out in post because it made the character "cross a line" that the director felt ought not be crossed. This is why there are almost no shots of Patrick Gates remaining in this scene: he was bleeding, and that's hard to hide. On a side note, the sweater he was wearing in the next scene had been ripped from the stabbing, and they were able to "unrip" his shirt with CG.
The code seen in Booth's Diary is an actual text encoded with Playfair method using the keyword DEATH. The complete text says: "La Boulaye lady will lead to Cibola temples of gold".
The man who had his Range Rover stolen by Mitch Wilkinson is costumer Hans Georg Struhar.