Rabbit, Run is suffused with religious questioning. Much of the religious debate in the novel relates to variations of Christian philosophy, but Freudianism (treated something like a religion), atheism, and a brief appearance, or rather, disappearance of the Dalai Lama provide interesting contrasts. Some of these perspectives are pretty risky for the McCarthy-ist and Red Scare era 1959 that provides the backdrop for Rabbit, Run. The drowning death of a newborn baby challenges the religious beliefs of many of the characters, and even provokes her father to dream of founding a new religion, based on "the truth" about life and death. The end of the novel does not tell us if he fulfills the dream’s prophecy.
Rabbit is constantly held up as a Christ figure in the novel. By doing this, Updike mocks the Christian idea of one man paying for the sins of an entire society.