In "Antipasto", Dr. Bedelia Du Maurier (Gillian Anderson) is seen drawing a two-tone SIG-Sauer P226 on Hannibal when he turns up at her house after the events of the Season 2 finale. In "Primavera", Will Graham (Hugh Dancy) is seen with his FBI issue P226 in a flashback.
Beretta 92FS
In "Primavera", Inspector Rinaldo Pazzi (Fortunato Cerlino) carries a Beretta 92FS as his sidearm, drawing it when he follows Will Graham (Hugh Dancy) into the catacombs of a cathedral in Palermo. In "Digestivo", several corrupt Florentine detectives working for the Vergers are seen armed with Berettas when they apprehend Hannibal and Will. An FBI agent at the end of the episode is also briefly seen armed with a Beretta.
Beretta 92FS Inox
Francis Dolarhyde (Richard Armitage) carries a suppressed Beretta 92FS Inox as his sidearm throughout the season, using it in "...And the Beast from the Sea" during his attack on the Graham household and "The Wrath of The Lamb" whilst ambushing a police convoy transporting Dr. Hannibal Lecter (Mads Mikkelsen. In "The Great Red Dragon", Will Graham (Hugh Dancy) uses the same gun during his mental recreation how Dolarhyde murdered the Leeds family.
Glock 17
During a flashback in "Aperitvio", Miriam Lass (Anna Chlumsky) is seen using Jack Crawford's Glock 17 shoot and injure Dr. Frederick Chilton. In "Dolce", Jack Crawford (Laurence Fishburne) is also seen briefly using a Glock 17 during his pursuit of Hannibal in Florence. In "And the Woman Clothed in Sun", a security guard at the Brooklyn Museum is seen with a holstered Glock 17. In "The Wrath of The Lamb", Baltimore Police Department officers killed by Francis Dolarhyde (Richard Armitage) are also seen with holstered Glocks.
Walther PPK
In "Digestivo", Mason Verger (Joe Anderson) briefly arms himself with a Walther PPK with light wooden grips. He later uses it to try and shoot Dr. Alana Bloom (Caroline Dhavernas), but is tackled by his sister before being able to do so.
Shotguns
Double Barrel Shotgun
In "Secondo", Chiyoh (Tao Okamoto) is seen hunting with a double barrel shotgun on the Lecter Estate in Lithuania. She later uses it to confront Will Graham (Hugh Dancy) when she finds him trespassing.
Rifles
Remington 700
In "Dolce", Chiyoh (Tao Okamoto) uses a suppressed Remington 700 to injure Will Graham (Hugh Dancy) to prevent him from stabbing Hannibal. She is later seen using the same rifle in "Digestivo", most notably to save Jack Crawford (Laurence Fishburne) from being killed by corrupt Italian detectives working for the Vergers.
Submachine Guns
Heckler & Koch UMP
In "Digestivo", a henchman working for Mason Verger (Joe Anderson) is briefly seen armed with a Heckler & Koch UMP as Hannibal and Will are delivered to the Verger Estate.
Heckler & Koch MP5A3
In "Digestivo", several FBI HRT officers who aid Jack Crawford (Laurence Fishburne) in arresting Hannibal Lecter (Mads Mikkelsen) in Virginia carry Heckler & Koch MP5A3's with underbarrel flashlights. In "The Wrath of The Lamb", an FBI agent guarding Dr. Alana Bloom (Caroline Dhavernas) and her family is also briefly seen armed with an MP5.
Other
X2 CO2 Dart Pistol
One of Mason Verger's henchmen guarding Hannibal (Mads Mikkelsen) is armed with an X2 CO2 Dart Pistol, which is picked up and used by Dr. Alana Bloom (Caroline Dhavernas) to subdue him.