Religion is usually not an issue in child custody proceedings, even if the parents practice different religions. For example, if a child has a Christian mother and a Jewish father, a court will not consider the merits of either religion in determining which parent should have custody of the child. The court will grant custody to one parent, or joint custody to both parents, and the child will be exposed to both the mother's religion and the father's religion.

In rare cases, religion will play a role in custody proceedings. One parent may claim that the child will be harmed by exposure to the other parent's religion. In such cases, courts must balance the right of each parent to control the religious training of the child against the best interests of the child. A court will resolve the conflict by determining whether exposure to the challenged religion will result in actual or substantial harm to the child. For example, a father claims that his child will be harmed by exposure to the religion of the child's mother because the mother's religion prohibits its followers from receiving medical treatment. In such a case, the court may grant sole custody to the father on the ground that granting custody to the mother would endanger the health of the child.

Generally, both parents will be free to instruct the child on religious matters, even if one parent is granted sole custody of the child. However, in some states, the custodial parent has the exclusive right to control the child's religious training. The noncustodial parent has no such right. In addition, if one parent proves that exposure to the other parent's religion will harm the child, a court may restrict the other parent's right to expose the child to the potentially harmful religion.