The film makes no verbal reference to the Divine Proportion, however, during a sequence in which Langdon cuts his face shaving, the pattern of the blood droplet in the sink vaguely resembles the shape of the Greek letter Phi. Also, the Bank of Zürich's emblem closely resembles a Phi.

In the film, Sophie found the hidden message near the Mona Lisa written at the bottom right of the painting. In the novel, it is written on the acrylic glass guard shielding the painting, making it appear as if it were written directly across the Mona Lisa's face.

In the film, Langdon deciphered the anagram, "So Dark The Con of Man," written near the Mona Lisa with the help of Sophie a few minutes after they found it while, in the novel, Sophie deciphered it when Langdon couldn't. 

In the novel, bank manager and friend of Jacques Saunière, André Vernet, turns against Langdon and Sophie because he has been waiting 20 years for somebody to return for the contents of the safe and believes they may have killed Saunière to access his valuables. In the film, Vernet's selfish interest in the contents are insinuated while, in the novel, a fuller explanation is given of his dedication to protect Saunière's interests as his client and friend.

In the film, Sophie's relationship to Saunière is not revealed to Vernet until he holds Langdon and Sophie at gunpoint. In the novel, she notifies Vernet that she is Saunière's granddaughter when they are in the bank. 

In the film, Fache meets Vernet in the hospital and tells him to turn on the homing device for the armored car while, in the novel, Vernet does so without informing Fache so that his bank's reputation would not be compromised.

The answer to Teabing's second question at the Château Villette gate is changed in the film. In the film, the question is put to Langdon whether he wants milk or lemon with his tea and Langdon responds that it depends on the type of tea they are having. In the novel, he is given the choice of milk or sugar and he hesitates before realizing that the correct answer is actually lemon and that the tea should be Earl Grey. In the film, when he is already in Teabing's residence he is offered this tea and asks for lemon to go with it.

No mention is ever made in the film of the surveillance equipment in the loft at the top of the barn at Teabing's manor nor of the miniature knight in Saunière's office in which a bug had been placed, although there is a glimpse in the film of the knight. Rémy Legaludec's criminal record is scrutinized by the police showing that he was kicked out of college for rewiring phone lines to obtain free service. This ties him into the plot as a surveillance expert. In the novel, the French police uncover Teabing's central role in bringing about the actions against the Priory of Sion. 

In the novel, Silas is portrayed as killing people because he believes that he is protecting the Catholic church. He is shown as killing with remorse; he knows it is a sin but that he is rescuing the church from possible ruination. In the movie, however, he does kill people with no sign of conscience or remorse at all. 

In the film, there is no second cryptex inside the first as there is in the novel and, in the film, the solution to the cryptex is the same as that for the second cryptex in the novel. 

The role of Opus Dei in the film is significantly scaled back and far less ominous than their portrayal in the novel. In the film, Aringarosa is a sinister member of a secret council of priests, called the Council of Shadows, dedicated to the destruction of the Sangreal and the living descendants of Christ instead of the desperate leader of Opus Dei dealing with the Vatican's desire to sever ties with it. 

In the film, Silas, Bishop Aringarosa, Leigh Teabing, Rémy, Opus Dei and the Council of Shadows all either know about or are responsible for the murders while, in the novel, only Silas, Leigh Teabing and Rémy are responsible for them. 

In the film, Opus Dei is portrayed as an organization trying to destroy the Sangreal while, in the novel, Opus Dei is trying to gain control of the Sangreal in order to wield more influence in the church. 

In the novel, after their escape with Teabing and the keystone, Rémy drops Silas off at the London headquarters for Opus Dei which is found at 5 Orme Court in Westminster. In the film, Rémy takes Silas to a non-descript "Opus Dei house." 

While the novel portrays Silas as a man in his forties, the movie makes him much younger by placing him in his mid-late twenties, possibly a move to make moviegoers sympathize with the young monk and his sad life. 

It is revealed that Bezu Fache is a member of Opus Dei in the film by his lapel pin ("the cross in the world") according to Langdon who sees it; this is not mentioned in the novel. In the film, Fache decides to pursue Robert Langdon on the basis of a false tip by Bishop Aringarosa whom he trusted—the Bishop told Fache that Langdon confessed to killing Saunière. In the novel, Fache learns of Silas from Aringarosa who tries to stop Silas from committing crimes as he realizes that he has been duped by the "Teacher." 

In the film, Langdon does not carefully hide the cryptex under a couch to prevent Teabing from discovering it prematurely the way he does in the novel. 

In the film, Teabing uses sophisticated computer animation to demonstrate codes in Da Vinci's aintings; whereas, in the novel, he merely points to the prints. Due to Teabing's uses of sophisticated computer animation with Leonardo da Vinci's The Last Supper, Teabing was able to digitally move Mary Magdalene's figure over to Jesus' left making it seem as if the figure is resting on Jesus' shoulder.  

The name of Rémy Legaludec, Leigh Teabing's butler, is changed in the film to Rémy Jean. The only exception to this is in the extended version in which a sequence is shown of Collet with another policeman. Collet refers to Remy Legaludec instead of Remy Jean. 

After Silas is killed in a hail of gunfire, in the novel Fache is sympathetic and compassionate towards Bishop Aringarosa whereas in the film he is vitriolic and spiteful. 

In the film, Rémy tells Silas that he is the Teacher while driving him to the London Opus Dei house; in the novel, Silas is given to understand that he is one of the Teacher's servants. In the film, Rémy is apparently poisoned by a pier in the Docklands of London while sitting outside the limo. In the novel, he is sitting in the front seat of the limo in St. James's Park with the "Teacher" when he dies as the result of an allergic reaction to peanut dust placed into a liquor flask passed to him by "the Teacher."  

In the film, Silas allows himself to be killed by police-assisted suicide in his remorse for shooting Aringarosa. In the novel, mortally wounded but still ambulatory, he flees the scene and goes to the hospital with the wounded Bishop Aringarosa who tells him to pray. He goes out into the hospital courtyard where he dies. 

In the novel, Robert and Sophie go to a library in London to discover the relevance of "A. Pope" while, in the film, they borrow someone's mobile phone (which had a web browser) on a city bus after they realize it will take too long to get to the library. 

In the novel, Sophie and Robert find a message scrawled on Newton's tomb with rubbing chalk telling them to go to the Westminster Abbey chapter house in order to save Teabing and it is there that Teabing reveals himself as the Teacher. In the film, Sophie notices Teabing's cane marks in the dust of the floor and Teabing reveals himself right at the tomb.

The revelation of the Teacher and the rest of the ending is presented differently. In the film, Langdon and Sophie discovered the Sangreal documents — and with them the secrets of Sophie's ancestry — hidden beneath the Rosslyn Chapel. In the novel, the documents are not discovered. Sophie, who is reunited with her grandmother and brothers (the "caretakers" of the chapel) is told by her grandmother that she is a descendant of Jesus Christ. 

The entrance to the tomb beneath Rosslyn Chapel is easily found in the film, marked by the symbol of the unified blade and chalice over the door to the passage. In the novel, no such entrance to the underground chamber exists and the chalice/blade symbol is less obvious as a sign worn into the floor of the chapel by the path walked by countless visitors. 

In the film, Sophie's parents and brother were killed in a car accident of unknown origin. In the novel, Sophie's brother survives and is raised by their grandmother at Rosslyn Chapel. In the novel, the grandparents agree to separate in order to protect the children. According to the novel, Sophie and her brother are reunited at the end–he is the guide or docent working at Rosslyn Chapel. In the film, the man working at Rosslyn chapel as a guide is not presented as her brother; her brother is said to have died in the car accident. 

In the novel, one of the most important aspects of Sophie Neveu's relationship with her grandfather, Jacques Saunière, is that she hasn't spoken to him in ten years. During those ten years, she never opened his many letters nor did she ever tell another person about her reasons. The novel presents Sophie coming to grips with why she was estranged from her grandfather. With Langdon's prompting her she comes to the realization that she accidentally witnessed a Hieros Gamos sex ritual involving her grandfather. In the film, this traumatic event is presented only as a flashback; we see Sophie looking in the windows of a door at masked men and women encircling a couple engaged in intercourse. Sophie realizes that the man of the couple is her grandfather. In the novel, Langdon explains this ritual to Sophie but, in the film, he does not. 

In the novel, Jacques Saunière is really Sophie's grandfather and she is reunited with her grandmother Marie who lives behind the Rosslyn Chapel with Sophie's presumed-dead brother, the docent. The novel has Sophie's grandmother tell Sophie that with great difficulty she and Saunière separated in order to protect the children by changing their family names and raising the two children in separate families. In the film, Langdon tells Sophie that Jacques Saunière is not her real grandfather on the basis of the Grail documents in the cellar of the Rosslyn Chapel. The docent is not shown to be Sophie's brother and a large number of protectors of the Sangreal with Sophie's grandmother meet her as she comes out of the crypt of the Rosslyn Chapel; all else is left unexplained in the film. 

In the novel, Robert and Sophie kiss at the end and plan to meet in coming months in Florence, Italy. In the film, while there are several moments of warmth between them, no romance is implied and they are shown making their farewells at the end. (This, of course, does not outright proscribe any such development between them; at the very least, a bond has definitely been forged between them.) 

In the film, Langdon tells Sophie that since the tomb of Mary Magdalene was apparently lost with the death of Saunière, it would not be possible to prove that Sophie is the last descendant of Jesus Christ and it may not necessarily be important or right to prove the bloodline. The choice was Sophie's. In the novel, Sophie's grandmother explains to Langdon that it was never the Priory of Sion's mission to reveal the "truth" about Jesus Christ and Mary Magdalene. Teabing's belief was that this was the priory's mission that he thought was thwarted by Jacques Saunière. 

In the film, Sophie playfully tries to walk on water and muses jokingly about turning water into wine, presumably because she was descended from Jesus. This sequence does not occur in the novel. In the novel, Leigh presents quotations from Leonardo da Vinci and many books including Holy Blood, Holy Grail. 

In the novel, Silas has red eyes and Sophie has green eyes. In the film, they have bright blue and brown eyes respectively. 

In the novel, Langdon is a firm believer in Grail lore having become a believer while researching his book Symbols of the Lost Sacred Feminine. However, in the film, he dismisses most of it as myth and even argues with Teabing about it several times. 

In the novel, Sophie's skill as a cryptologist is reiterated again and again, showing that she is adept at solving riddles, anagrams and puzzles while, in the film, it was only mentioned once in the beginning at the Louvre. 

At the end of the film, a stubborn Aringarosa is placed under arrest by Fache as he is carried into an ambulance. In the novel, an innocent, though remorseful, Aringarosa arranges to have the bearer bonds he acquired divided among the families of Silas's victims as he lies recovering on a hospital bed. 

In the novel, when Teabing and the rest are escaping from France, they call the pilot and say they need to go to London. In the film, Teabing has his pilot fly to Zürich, Switzerland, from which Langdon and Sophie could not be extradited back to France. When Langdon finds a secret message on the crytex's rosewood box mentioning London, Teabing has the pilot change course for London. 

In the novel, Teabing claims that over 3 million women were burned at the stake during the witch trials. In the film, it is Langdon who first posits the figure of 50,000 people and Teabing who goes on to add that "some people say much more, possibly millions." 

In the novel, Teabing's claim that Emperor Constantine invented Christ's divinity is met by Langdon with a "soft nod of concurrence." In the film, Langdon passionately challenges this claim of Teabing's. 

While the novel represents the Christians as waging war on the pagans in an attempt to suppress them, in the film, this claim of Teabing's is countered by Langdon that it is unknown whether it was the Christians or the Pagans who initiated the violence. 

In the novel, Sophie reads from the Gospel of Philip that "Jesus loved Mary Magdalene more than the other disciples and kissed her often on the mouth". In the film, Teabing reads the passage out loud but is significantly cut off by Robert just after the words "often on the—!" 

In the book, Langdon and Teabing agree unanimously on the existence of the Priory of Sion and its nature. In the film, Langdon challenges Teabing, stating the Priory was proven to be a hoax, which Teabing retorts is "exactly what they want you to think". 

In the novel, Sophie has red hair, reinforcing her connection to Mary Magdalene but the actress in the film (Audrey Tautou) is a brunette. 

In the film, there is no mention about Langdon’s Mickey Mouse watch, although it does make a brief appearance in the sequence of Langdon and Sophie in the back of the armored van. 

In the film, Robert Langdon discovers the path to the real location of the tomb of Mary Magdalene from shaving and a book he wrote. In the novel, it was mentioned that Langdon was writing a book and his editor had sent out copies, one which Saunière had read, which was the reason why he had made an appointment with Langdon before his death. Realizing that he had written something about how an object in the Louvre appears like an iceberg, as it is depicted in the film in the end, he was in shock to find that as he stood inside the Louvre over Mary Magdalene's tomb, he had known the location all along.

The novel contains a sequence in which Sophie and Langdon escape from a museum guard by Sophie threatening to destroy a Da Vinci painting. This scene is not in the theatrical release of the film, although it was filmed and images from the scene are included with the published screenplay. It is restored to the film entirely on the Extended Edition DVD. 

In the novel, Collet is implied to be a younger and barely-tolerated subordinate of Fache's. In the film, he is depicted as being of a similar age and being both colleague and friend to Fache. 

The film emphasizes Sophie's spirituality considerably more than the book (almost telegraphing her ancestry). For example, during the armored car escape, she is shown "curing" Langdon's claustrophobia as if by touch and in another scene she gives a junkie money in exchange for privacy, trusting that the man won't simply buy more drugs. Neither incident occurs in the novel. 

Bezu Fache severely beats an air traffic controller in the film; he does no such thing in the book. 

In the novel, Sophie's Smart Fortwo is red but in the film her car is grey. 

In the novel, Silas drives a black Audi. In the film, if one looks closely during one scene, Silas is instead driving a Renault. 

In the film, it is said that Langdon prayed to Jesus to save him from the well. In the novel, there is no scene about this.