In Doubt, the main doubt in the movie is not of faith but rather doubt about the nature and innocence of the parish priest Father Flynn. The doubt is two-fold, as we see the doubt of Sister James, who isn’t as sure as Sister Aloysius through the film, and her doubt reflects our doubt about the circumstances in the movie. It is never clear in the movie if Father Flynn is guilty of sexual abuse or misconduct—so any images or hints we are given create doubt in us as an audience.

The Eye of God

One of the critical images we see in the movie is the large stained-glass window in the church that shows the eye of God peeking out of the clouds. The eye is a representation of the concept that God can see all—which casts doubt on the innocence of Father Flynn, as he makes a face of shame when he looks at the eye. This scene is crucial because it is a private moment where we get to see Father Flynn react to the image. However, it is important because, though it casts some aspersions on Father Flynn’s innocence, it isn’t clear what he is ashamed about, and thus it creates further doubt in the movie.

Knowing Looks

There are several places in the film where Father Flynn and Donald Miller share looks at one another that appear to show some form of secret connection. Sister James catches many of these knowing looks and sees the imagery created by the looks on the actors' faces, and it leads to her doubt. Along with causing doubt for Sister James, the knowing looks and close relationship between the two makes the audience question their own thoughts about the relationship.

The Bird

There is a bird in the movie that is seen trapped in a tower of the church. The bird is an image that represents Donald Miller, as he is the one who notices the bird during the mass. This image creates doubts in the mind of the audience about Donald’s feelings toward the church and toward his place at the school. Does he want to escape because he is a closeted homosexual or is it because of the abuse he suffers at the hands of Father Flynn?