- In the DVD Behind The Scenes featurette we see Hannibal actually cutting into Krendler's brain during the climactic scene, whereas in the released version only Clarice's reaction is shown.
- A different version of Clarice watching Brigham's funeral on TV. Here, she doesn't cry, but rather just sits staring at the screen. Another FBI agent comes to visit Clarice with all of Brigham's personal belongings, saying that his parents don't want them, and Clarice asks if she can have them.
- A new scene where Starling visits the abandoned asylum where Hannibal Lecter was held. At the door she meets the janitor, a shy young boy who flirts with Starling but refuses to go into the basement because of asthma. Starling goes down into the basement, where she searches old patient files, and finds a vagrant old man huddled in Lecter's old cell screaming for Jesus. Later, we see Starling on Ebay searching for Hannibal Lecter items, among which are X-rays and Lecter's Mercedes.
- A new scene where Starling gets a follow up on the X-rays she got from Barney and Mason. An FBI specialist tells her that Mason's X-ray is several years old, and that Barney's X-Ray of Lecter's broken arm is the most recent.
- An alternate version of the scene where Lecter writes a letter to Starling. We see Lecter going to pick up the scent for the envelope, where Pazzi spies on him and, in turn, Lecter spies on Pazzi. The letter itself is worded differently, but still contains the lines about Starling's parents. Here, we learn that Jack Crawford, Starling's old boss from the FBI, died of a disease. Hannibal assures Starling in his letter that he observed a moment-and no more-of silence. We also see Lecter sealing the letter with ink, and dropping the letter off at a mailbox, with Pazzi watching him. The entire scene is accompanied by music composed and played by Anthony Hopkins.
- A scene where Pazzi gets FBI passwords from a secret agent holed up in a building in Italy.
- An ignored subplot about Pazzi and a brother-sister gypsy pickpocket team. The sister was a girl named Romula, who Pazzi saw steal a man's wallet. This was the only sequence filmed, which was scrapped in favor of just leaving in the brother as the thug Pazzi sends after Lecter.
- An entire subplot about Pazzi working on Il Mostro, a real unsolved Italian serial killer case in which an unknown man stalked and killed young couples kissing in their cars. It features an alternate version of the scene where Lecter first meets Pazzi--now there is a leering janitor waxing the floor in the next room. Pazzi talks at great lengths with Lecter about Il Mostro, and Lecter gives him information regarding the case, most notably that the killer is posing his victim's corpses like classic paintings. Pazzi follows this lead, which gets him put back on Il Mostro after being removed to investigate Dr. Fell. Later, when he goes to retrieve luggage from Lecter, we have an alternate version of Pazzi in Lecter's living room, with more talk about Il Mostro. All of these sequences feature the janitor from the museum. Finally, we are given an alternate version of Lecter attacking Pazzi. The dialogue is slightly different, and there are several shots of the janitor watching. Here, Pazzi's intestines and bowels don't fall onto the spotlights, and the tourists videotaping the tower laugh instead of scream. Lecter turns around and waves at the tourists, and then walks away. Meanwhile, we see several shots of security looking at Pazzi's body on security cameras as Lecter passes by the Janitor, who had been watching the whole thing from behind it a curtain: He is Il Mostro.
- A deleted scene in which Barney drives through Mason's plantation. Originally, the movie was supposed to open with the fish market shootout, and the meeting with Mason was to come later. When the meeting was moved to the opening, the scene was Barney in his car was cut: It features him going past security and men reaping vegatables. The box containing Lecter's restraint mask is visible in several shots on the seat beside Barney. Lastly, Barney comes across the man-eating boars in a pen and drives away from them.
- A brief shot of Lecter sleeping on an airplane with his head shaved. He has a nightmare and wakes up almost screaming. This came from the book, in which Lecter had flashbacks to WWII, when his two-year-old sister was killed in a snowbound concentration camp in Austria and eaten for food by starving Nazis.
- Scenes of Lecter shopping for his party. He goes to a kitchen store, and catches a tabloid show talking about Starling. A humorous bit is included in which Lecter gets angry because the TV commentator addresses him as "madman Hannibal Lecter," and he corrects her by whispering at the TV "Doctor Lecter!" A clerk then comes in and directs Lecter to where he can buy steakknives. Lecter then finishes watching the program, where he sees an interview with Krendler.
- An extended version of Clarice in the woods. She runs for a longer period, and shots of her feet on the ground are intercut with Lecter's feet. After the part where the scene would've ended in the final cut, we see Lecter standing by Starling's car on a hilltop. He breaks the lock and gets in, smelling her steering wheel and then running his tongue across it. He gets out, but leaves his sun glasses on the horn.
- An alternate ending: Here, Starling doesn't handcuff Lecter, and he runs his tongue over her lips after they kiss. Starling gets her hair free from the refrigerator, gets her gun, and runs out to the woods after Lecter. She finds the boat drifting and draws her gun on it, but it's empty and she smirks for a moment before she's surrounded by police who have her drop her weapon. A spotlight hits Starling and she yells "Clarice Starling! FBI!" The scene then cuts to Starling watching the fireworks over the lake, as in the original. Here, though, instead of cutting to the plane, we see Lecter walking up to a gas station and getting into a van. He waves at some kids and their mothers waving sparklers, and drives off. This goes to a wideshot of the plane cabin, showing most of the passengers and waitresses to be Oriental (implying Lecter is headed to Japan, Korea, China, etc.) The wide shot cuts to the young boy coming out of the bathroom and finding Lecter with his food. They have the same conversation as in the finished version, but only up until the boy asks for food. Here, Lecter asks the boy if his mother ever warned him about taking food from strangers. The boy says she has, but Lecter smiles and says that it doesn't matter since the boy's mother is asleep. Lecter then feeds several forkfulls of the brains to the boy before the screen freezes, with the back of the boy's head superimposed over half of Lecter's face. Commentary by the director says that the scene as it is viewed here was meant to be symbolic, showing Lecter corrupting the boy.