Waits doesn't have a religion and some of his comments point to agnosticism.
We know he's pro-choice, which places him in the Democrat/liberal camp.
There's something spiritual about Tom Waits' music, something that evokes images of Southern Baptist revivals and bayou exorcisms, maybe even Voodoo. But he's not Southern, unless you count Southern Californian–possibly the most nonreligious region of the United States. He was born in Pomona, California and grew up near San Diego.
Religion played a very small role in Waits' upbringing, even though his father was of Irish descent–indicating there was probably at least a bit of Catholic influence.
Waits has always danced to the beat of his own drum, and he confirms that religiously when he sings his song, "Chocolate Jesus," saying:
I don't go to church on Sunday, don't get on my knees to pray, or memorize the books of the Bible, I got my own special way.
Though he does not articulate what his own way is.
Waits' major theological contribution is to deny the existence of the Devil. He sings:
Don't you know there ain't no devil, it's just god when he's drunk.
It's an interesting idea. A drunk, mischievous God tempting the impressionable people of the world to wickedness.
Waits, though seemingly non-religious, did once play a benefit concert for Tibetan Buddhist monks, indicating that he's at least sympathetic to their cause. Asked why he did the gig, Waits responded with his classic dark humor, saying:
I'm no fool. It's a spiritual insurance policy.
This is the sort of comment that would come from an agnostic, one of the philosophy that "I better just believe in religion, because if there is a God, I don't want to be on the wrong side of Him."
A true artist
Waits isn't very outwardly political either. Obviously a man like that has his opinions and the closest we get to hearing them are in his songs. His song "The Day After Tomorrow" is an Iraq War protest song told from the point of view of a soldier who's about to be sent home. The soldier knows the war is based on lies and Waits sings:
I'm not fighting for justice/I'm not fighting for freedom/I am fighting for my life and/Another day in the world here.
Waits sees society through the lens of an artist. Art should not be commercialized in his view, it is sacred and personal. Waits has even sued–and won–various large corporations like Frito-Lay after he refused to sell them his music for advertisements and they used "soundalike" artists.
In today's political environment, we can be sure Waits would oppose the anti-birth control zeitgeist of the Republican Party. In 1993, Waits contributed a song to the "Born to Choose" compilation disc for women's reproductive health charities.