Religious belief is often discussed on House, M.D., generally in the context where faith and belief contrast with science and logical analysis. Several episodes explore the religious beliefs of the characters, the patients, and other ancillary characters.
Despite the fact that House self identifies as an Atheist and berates all forms of superstitions, he has shown minor signs of agnosticism or spirituality. In Brave Heart, before going to sleep, he secretly began to speak to his deceased father on his bed about how he has been focusing on only hating him and admitted they did have some good times as well, but berated it after he realized that Wilson can hear him across the room, much to Wilson's pleasure. Wilson then speaks to Amber and states that House is indeed getting better.
Atheism is the religious stance most thoroughly explored on House, and Gregory House, Eric Foreman, and Allison Cameron have all identified as atheists. House and Foreman both had religious upbringings (in a Protestant faith, most likely Methodist for House), and only came to leave religion once they started in the medical profession. Cameron's religious upbringing is unknown.
House consistently rejects anything but a rational explanation for seemingly wondrous or miraculous occurrences (see, in particular, 97 Seconds, Here Kitty, and Human Error). Even in Unfaithful, when an atheist priest re-finds his faith due to a series of good fortune, House puts it down to massive coincidence.
That being said, House is not above portraying himself as a miracle worker (although a falible one). He often uses religious language after coming to an "epiphany" (which is used more often to describe these moments than the more secular "eureka moment") and describing to the patient how they are about to be "miraculously cured".
Several characters on the series self identify as Jewish, including Lisa Cuddy (on her father's side), James Wilson (on his mother's side) and Chris Taub (and his ex-wife Rachel Taub). Despite their religious beliefs, none of the regular Jewish characters on the show are highly observant and act more akin to a deistic faith system. Wilson, for example, eats bacon and ice cream, and Cuddy has only became strongly observant of Judaism after the adoption of her child Rachel.
There are few other Jewish characters on the show, but two of the most notable were in the episode Don't Ever Change - Roz and her husband Yonatan. The couple created a great contrast for House - one being a lifelong Hassidic Jew, the other recently embracing it in her forties. House's suspicion about religion made him believe Roz's conversion was a symptom of her illness (it was, in fact, unrelated), but enraged the husband. However, later on, it is Roz's faith that threatens her treatment, while Yonatan wants to work to convince her that her that the Torah commands that life is more important than the religious laws.
Robert Chase is the only openly religious character on the team, and he clearly identifies as Catholic. Despite what he called his crisis in faith and his embrace of a secular life, it is clear that he has never left it behind and often draws from it.
Many patients have been Catholics and, for the most part, House tends to be more respectful to Catholics rather than those of other faiths. It could be because they often tend to be his intellectual equals and are more likely to be able to engage in discussions about faith with him. Typical of this is his conversation with Sister Mary Eucharist in Damned If You Do, where they both challenge each other's commitment to their beliefs, but in a respectful manner with mutual admiration.
Although the various Protestant faiths are the most common among the American public, none of the main characters clearly identifies as a Protestant, and even fewer patients are so identified. In cases where the patient is clearly Protestant (such as Boyd in House vs. God), House is openly dismissive.
However, it is also clear that House's biological father is a Protestant as well - a Methodist minister. House's antagonism to religion could be based in the "big lie" in his life - that John House is House's actual father. Above all, House has never been a big fan of hypocrisy, and this probably makes him all the more suspicous of openly religious people.