The Vatican has an absolute prohibition on sterilization for the purposes of birth control. The U.S. Catholic bishops consider the procedure "intrinsically immoral," on par with abortion. Yet for years, Genesys Health System, a Catholic medical center near Flint, Mich., allowed doctors delivering babies there to tie the tubes of new mothers who wanted to ensure they never got pregnant again.

Genesys's policy wasn't hard to fathom: Performing a tubal ligation immediately after childbirth is the long-established standard of care, especially if a woman is having a cesarean section. "She's already cut open — her tubes are right there," said Sarah Ward Prager, an associate professor in obstetrics and gynecology and director of family planning at the University of Washington Medical School. Subjecting a new mother to a second surgery carries "unnecessary risk," Prager said. "It is simply unethical to say, 'I'm going to make you come back to a different hospital to have another surgery in six weeks because the bishop says I can't tie your tubes right now."

Then, seemingly out of the blue, Genesys reversed course. Starting November 1, sterilization with the "direct" aim of preventing pregnancy — as opposed to for some other medical ("indirect") reason — was banned. Patients who had planned to have the procedure after childbirth were left scrambling; their irate doctors were, too.

Genesys won't say why it allowed sterilizations to go on for so long or why it has forbidden them now. In a statement to ProPublica, the hospital acknowledged only that it had "updated its policy on tubal ligations to comply with current Church teaching."

But this much is clear: The Genesys decision is almost certainly a sign of things to come.

In November, the U.S. Conference of Catholic Bishops voted to tighten its rules on partnerships and collaborations between Catholic and non-Catholic health care providers. The move has potentially sweeping implications for patients, doctors, and medical providers in thousands of communities from New York to California.

As the new rules are hammered out in the coming year, the policy on tubal ligations will be a central issue. Concern over how some Catholic hospitals have been accommodating secular health care partners that want to continue doing postpartum sterilizations is at the heart of why the Vatican and the American bishops are pushing to revise the Ethical and Religious Directives for Catholic Health Care Services. Those directives govern care at every Catholic-sponsored hospital, clinic, nursing home, and health-care business in the United States. They are also meant to cover the joint operations of merged Catholic and secular health care facilities..

Many women's health advocates worry that a further restriction of tubal ligations could affect not just patients and doctors today but well into the future. "Physicians who receive their training in Catholic institutions are not getting trained in this basic procedure," said Debra Stulberg, an assistant professor in family medicine at the University of Chicago who has studied the role of doctors in Catholic systems. "You are sending them out to provide obstetric and gynecological care without a full set of tools in their toolbox."

Amid the escalating conflicts over reproductive rights, tubal ligations haven't generated nearly as many headlines as abortion. But many doctors and patient advocates feel strongly about the topic — especially their ability to provide the surgery to a new mother immediately after childbirth. Obamacare's requirement that insurers cover sterilization along with other forms of contraception has further inflamed passions.

Tubal ligations are the second most common form of birth control used by American women (just slightly behind the Pill) and by far the most popular method among women in their 30s and 40s, according to new data from the CDC. An estimated 700,000 tubal sterilizations are performed in the U.S. every year.

In this country, approximately half the women who get their tubes tied have the procedure in outpatient settings; the rest have it in hospitals following the delivery of a baby. Because of the position of the uterus after childbirth, postpartum sterilizations are easier to perform, they don't add any recovery time, and they are almost foolproof, Prager said.

If a woman can't have her tubes tied immediately after delivery, she must wait until her body has healed — generally six weeks. At that point, the hurdles to having the procedure — a newborn and family to care for, insurance and other financial issues, a lack of maternity or sick leave — often lead to women abandoning the idea. Meanwhile, other forms of birth control may not be as reliable. In one study of new mothers in Texas who were denied a tubal ligation after childbirth, nearly 50 percent had an unplanned pregnancy within 12 months. "It's not just a convenience thing," said Prager, who is vice chair of the American College of Obstetricians and Gynecologists' Committee on Health Care for Underserved Women. Denying postpartum sterilizations "has very real consequences for entire families," she said.

The discontent among doctors has increased in recent years, as Catholic healthcare has seen explosive growth and partnerships between Catholic and secular providers have become both more common and more complicated. Ten of the 25 largest health systems in the nation — and four of the five largest nonprofit networks —are now Catholic-sponsored.

Doctors often wind up confused and frustrated  by the constraints laid out in the Ethical and Religious Directives. The ERDs ban "direct sterilization of either men or women, whether permanent or temporary," but allow "procedures that induce sterility ... when their direct effect is the cure or alleviation of a present and serious pathology and a simpler treatment is not available."

The ERDs also lay out guidelines for Catholic health care institutions as they merge or collaborate with other organizations. A key requirement: when Catholic and secular health organizations merge or affiliate, the non-Catholic partner must agree to "respect church teaching and discipline."

Most of the time, this means that secular hospitals have to stop providing sterilizations to new mothers who want them except in very limited circumstances. These restrictions "are usually the key flashpoint for community activists who oppose" Catholic and non-Catholic health care partnerships, said Lois Uttley, director of the nonprofit organization MergerWatch.

But in recent years, a few Catholic providers in some parts of the country — and the local bishops who oversee them —have taken a more flexible attitude. "The Catholic health system says, 'We will have nothing to do with the community hospital if they perform abortions, but since tubal ligations are not so grave ... they can go ahead and do that,'" John Haas, president of the National Catholic Bioethics Center, recently told the National Catholic Register.

In Troy, N.Y., for example, when several Catholic and non-Catholic health systems merged, a separate, secular maternity hospital was established on the second floor of a Catholic hospital to allow doctors to continue providing sterilizations and prescribing birth control. In California, the Catholic Healthcare West system severed some of its ties to the church and changed its name to Dignity Health — all with the goal of allowing secular hospitals that merged with the system to preserve reproductive services, including sterilization.

As the rapidly changing health care market forces an unprecedented wave of mergers and collaborations, looking for creative ways to preserve access to sterilization makes sense for Catholic health care companies as well as doctors and patients, Uttley says. "Maternity services can be a big generator of patients," she said. "If they are restricted in some way, it makes the hospital a little less attractive for women and their families. They'll choose a different hospital if they can."

Meanwhile, as the Genesys incident highlights, Catholic hospitals themselves have sometimes taken a more liberal interpretation of the rules — or perhaps just been confused about when tubal ligations are permissible.

In 2011, Sandra Hapenney, a biostatistician then earning her doctorate in church-state studies from Baylor University, analyzed patient data from every Catholic hospital in seven states, including California, Texas, Illinois and New Jersey. Her discovery: From 2007 through 2009, nearly half  the hospitals had allowed doctors to perform postpartum sterilizations — more than 20,000 procedures in all. "There was a kind of skirting around the ERDs and interpreting them to say that tubal situations in certain situations could be considered indirect sterilization" — for example, if another pregnancy would harm a mother's emotional state— she said.

The findings came as a surprise to many bishops (although not necessarily to conservative Catholics, as this intriguing study uploaded to Wikileaks shows). "There was quite a bit of pressure on the bishops, and some of them [in Texas and California, for example] reacted immediately to get their hospitals to stop performing [sterilizations]," Hapenney said. "Other ones have acted quietly."

Indeed, a commentary by Father Tadeusz Pacholczyk, director of education at the National Catholic Bioethics Center, takes a decidedly hard line:  Sterilization, he wrote, is only permissible if,  "in treating an existing medical problem ... [it] brings about an unintended loss of fertility in the process." A tubal ligation to prevent a future pregnancy that might harm a mother's mental state — or even endanger her life — does not fit that criteria, Pacholczyk wrote, suggesting that a couple could instead practice "periodic abstinence to avoid a potentially dangerous pregnancy." He added, "[c]utting healthy fallopian tubes in a woman's body is never a morally defensible medical decision."

That view may have some sway as the U.S. Conference of Catholic Bishops works over the next few months to revise the ERDs as they relate to mergers and partnerships. The goal, the USCCB has said, is to incorporate Vatican principles ensuring that Catholic institutions do not "cooperate immorally with the unacceptable procedures conducted in other health care entities with which they may be connected" or "cause scandal" as a result of such collaborations.

In the case of Genesys, however, civil rights groups and women's advocates argue that the hospital's sudden end to tubal ligations is the real scandal. Most obstetricians had admitting privileges only at Genesys, which left them little choice: Perform the sterilization at a later date, risking infection and other side effects, or prescribe a form of birth control that might not work as well.

The ACLU of Michigan has filed a letter of complaint with the state Bureau of Health Care Services, saying that the Genesys move violates state law as well as federal Medicaid and Medicare patient protections. "To ensure patient safety, hospitals that are open to the public and participate in government programs must be held to the same quality medical standards regardless of their religious affiliation," ACLU staff attorney Brooke Tucker wrote.

Meanwhile, in its statement to ProPublica, Genesys stressed that it has not stopped performing all tubal sterilizations. "[Those] performed for medical purposes, such as prophylactic salpingectomies for reducing the risk of cancer, are not directly contraceptive in their purpose, and could be permissible, depending on prudent medical judgment and the informed consent of the patient," the hospital said.

Related coverage: For more, read about the USCCB vote to revise rules for health care partnerships.