Alternate versions

The DVD release offers several scenes that were edited, reshot, or removed altogether after poor test screenings. Glimpses of several of these scenes can be seen in the movie's original theatrical trailer (also included on the DVD):

• An alternate opening where Father Almeida commits suicide by jumping off of the roof of his church. In the final cut, there is no indication as to how he died.
• A longer, much more explicit version of Frankie and her boyfriend Steve fooling around during the opening credits.
• Before Frankie's first stimagtic attack, she experiences a series of strange occurances while closing her hair salon.
• Also, before Frankie's first stigmatic attack, she comes home and is scared by her boyfriend Steve. The two have an argument.

A single shot of Jennifer and Steve looking at Frankie after she stands up and runs out of the club was not included in theatrical release but appears in most dvd/video release version.

The DVD features an optional director's alternate ending from the theatrical version. In the scene near the end after Frankie (Patricia Arquette) is freed from her affliction, Father Kiernan (Gabriel Byrne) carries her outside in his arms and sits at a bench, and we see her collapse in his arms. He looks up to see her holding a bird in her hand, then she walks away. After she apparently walks away, he looks back down to see her lifeless body still in his arms -- she actually died from the fifth stigmata and he watched her soul depart. In the theatrical version, after she walks away with the bird, Father Kiernan is left alone on the bench, and the impression is that she's "cured" and lives the rest of her life naturally.

It is important to note that in the director's alternate ending, Frankie suffers the fifth wound of Christ (or stigmata) -- the piercing of the side. Earlier in the movie, Father Kiernan suggests that only the most pious receive the wounds of Christ and that the more wounds they receive, the more pious they are. He also says that no one has ever received all 5.

In the mentioned alternate ending, after Frankie dies, we see also an alternate, extended shot of Father Kiernan discovering the secret scrolls, in it he also places a picture of Frankie in front of the statue. The ending text about the scrolls is intact.