Other sources maintain that Scientology is not an issue in the split. Tom Cruise, who has not yet answered Holmes's divorce filing, is a longtime Scientologist and advocate for the sometimes-controversial church, and his older children, Bella, 19, and Connor, 17, were raised in Scientology.
So what is life like for a child being raised in the church – and what would be next for Suri if Scientology stays part of her life?
The influence starts early: Scientologists encourage a pregnant woman to have a "quiet birth" to prevent unwanted emotions and irrational fears from being recorded in a child's subconscious mind. Cruise told GQ in 2006, "It's really about respecting the woman. You want to keep things as calm as possible."
While breast-feeding is fine, church founder L. Ron Hubbard personally developed a recipe consisting of barley water, milk and corn syrup that he recommended for infants. Hubbard recommended it as "a healthy, natural alternative to store-bought 'formulas,' " says Scientology spokesperson Karin Pouw.
After birth, the parents hold a naming ceremony for the child. The infant is welcomed by the congregation, and their parents and godparents pledge to care for the child and allow them to choose their own path in life.
Older ChildrenAs children grow up, they're encouraged to make decisions for themselves.
"Everything needs to be positive and open so a child can experiment and go away from learning situations with positive thoughts and ambitions," says a Florida church member who has studied with Cruise, adding, "Children should never be held back or discouraged from following their bliss. Parents should not get in the way of what a child wants to do."
In fact, one Scientology handbook states, "Children are not dogs. The sweetness and love of a child is preserved only so long as he can exert his own self-determinism." And in his 1950 book Dianetics, Hubbard wrote, "A child needs all the love and affection it can possibly get."
But Scientology spokesperson Pouw disputes the notion that parents are advised never to tell children "no."
"It's not true that a child can do anything he or she wants to do. Parents who are Scientologists most certainly instruct their children in things they may or may not do and could certainly say 'no.'"
Parents are also encouraged to react calmly when a child is injured. As actress Leah Remini, Cruise's friend and a fellow Scientologist has told PEOPLE, "We just give them a second and try not to gasp. You console them, but you don't do the initial 'Aaah!' They might not react as much if your reaction isn't as big. It's about letting them be self-determined but in a safe environment."
Mario Anzuoni / Reuters / Landov
Confessional AuditingOlder kids start undergoing "confessional auditing," or "sec checks," a central part of Scientology in which followers answer questions while hooked up to "e-meters" that register lie-detecting impulses milling around the body. According to a recent series of articles in the Village Voice and Paulette Cooper, author of a critical book called The Scandal of Scientology, children can begin the "sec checks" around Suri's age, answering questions such as "Have you done anything you are ashamed of?"
But Scientology disputes that kids as young as Suri normally undergo auditing. "It is not true that it is a standard practice that children of Scientologists begin 'sec checks' at the age of 6," Pouw says.
Pouw says she is unaware of a child as young as 6 going through the process, though she says it wouldn't be "abnormal," comparing it to confessions in the Catholic church that begin at a young age.
"With respect to children, Mr. Hubbard gave the ages of 12 to 15 as those most suitable to begin auditing," she says.
As for rumors that Holmes is concerned Cruise would enlist Suri in Scientology's military-like Sea Org, Gary S. Soter, an attorney for the church, calls them "preposterous and untrue. ... No person younger than age 16 is accepted in the Sea Organization. Further Church policy requires the consent of both parents and/or all legal guardians. There are no exceptions."