Gilligan explained that when he was developing the drama he wanted to focus on the effects of people's behaviour.
"If there's a larger lesson to Breaking Bad, it's that actions have consequences," he told the New York Times.
"If religion is a reaction of man, and nothing more, it seems to me that it represents a human desire for wrongdoers to be punished. I hate the idea of Idi Amin living in Saudi Arabia for the last 25 years of his life. That galls me to no end."
Gilligan continued: "I feel some sort of need for biblical atonement, or justice, or something. I like to believe there is some comeuppance, that karma kicks in at some point, even if it takes years or decades to happen."
Gilligan, who has previously suggested that the show could end after five seasons, also revealed that he finds it draining writing Walter White (Bryan Cranston).
"It's hard to write a character that dark and morally ambiguous," he said. "I'm going to miss the show when it's over, but on some level, it'll be a relief to not have Walt in my head anymore."
Breaking Bad will return for a new season on July 17 on AMC.
Watch a trailer for the fourth season of Breaking Bad below: