Some of the footage of the subway car is from Money Train (1995). You can actually see the steel beam sticking out of the front window.
To anyone who's ever trained (or even fed) birds, it's obvious the doves flying into Frankie Paige's hands are eating from her palms.
Patricia Arquette's character is named Frankie (short for Frances), similar to the name of the saint, Francis, whom we're told by Gabriel Byrne's character was the first to receive the stigmata.
The body of Almeida in the coffin actually was a wax dummy made in Los Angeles and shipped to the filming location.
When we see inserts of the crucifixion, while Frankie as her first attack of stigmata, the arms being nailed are rubber arms with wires that make the fingers slightly move.
The subway scene was shot on a fake train carriageway - the same one used sometimes in Seinfeld.
When Father Kiernan (Gabriel Byrne) comes in the Vatican office to get is new assignment, we can hear a bit of Italian speaking in the back between Cardinal Daniel Houseman (Jonathan Pryce) and another priest. Translation: "Rest assured, none of this will never leave this room."
During the final scene in the garden, the statue in the background is of Saint Francis of Assisi, the first person to bear the marks of the Stigmata.
The producers and director 'Wainright, Rupert' originally were thinking of calling the film, St. Frances of Pittsburgh
Patricia Arquette was Rupert Wainright's first choice to play Frankie.
The phrase "Split a piece of wood; I am there. Lift up the stone, and you will find me there." comes from the "Gospel of Thomas" (Verse 77).
The "Aramaic" Frankie writes on the wall, is actually ancient Hebrew, because Rupert Wainright thought looked more intriguing.
The Gospel of Thomas is a real historical document that some believe to be the actual words of Jesus to his disciples; however, the real-life document was written in Coptic, an ancient Egyptian language based on the Greek alphabet, not Aramaic, as the movie states.
When discussing the five stigmata, Frankie refers to the spear in Jesus' side as "the one that kills him." However, the spear was used to be certain that he was already dead.