After Holden's prostitute leaves him in chapter 14, he is alone in his hotel room getting ready for bed. He suddenly gets the urge to pray and says the following:
"I felt like praying or something, when I was in bed, but I couldn't do it. I can't always pray when I feel like it. In the first place, I'm sort of an atheist. I like Jesus and all, but I don't care too much for most of the other stuff in the Bible" (99).
One can infer that Holden has had some religious influence in his life if he feels like praying; but, it must not have been habitual growing up because he doesn't say that religion is a big part of his family's life. In fact, his parents are different religions and he claims all of their children are atheists.
It's funny, though, where Holden's thoughts take him after feeling the urge to pray. He thinks about the "Disciples" and how much they annoy him. He likes Jesus, but he thinks that the twelve apostles let him down during his lifetime. He says, "they were about as much use to Him as a hole in the head" (99). He does like a lunatic who lived in some tombs and was cutting himself, which is interesting. Holden likes the lunatic more than the apostles.
Then Holden discusses a religious boy he knew at the Whooton School named Arthur Childs. Arthur tells Holden that he should like the "Disciples" because Jesus chose them to represent him after he left. Next, their conversation turns to talking about Judas betraying Jesus. Arthur says Judas is surely going to Hell, but Holden says that Jesus would forgive him. Arthur tells him that his problem is that he doesn't go to church, which he concedes is true. Therefore, Holden seems to be spiritual in a sense because he believes Jesus would forgive Judas. However, he doesn't go to church, he doesn't like ministers, and he feels he is atheist--and yet, he feels the urge to pray.