The report quoted doctors who said they saw patients become gravely ill when hospitals refused to terminate their nonviable pregnancies, causing infection to set in. It also quoted women who wanted a tubal ligation to prevent future pregnancies at the same time that they delivered babies, when the procedure is easiest, but were told that they would have to go to another hospital to get the procedure separately because their births were at Catholic centers.

More and more hospitals are run by Catholic institutions, as health-care systems across the country merge to alleviate financial burdens. The ACLU and MergerWatch, an organization that advocates for local communities when hospitals merge, previously reported in 2013 that 1 in 10 acute-care hospital beds were in Catholic-owned or -affiliated hospitals.

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The jump to 1 in 6 beds is partially the result of hospital mergers, but also because of a change in how the new paper categorized Catholic hospitals. Rather than looking at only Catholic nonprofit hospitals, the organizations also looked at government and for-profit hospitals managed by Catholic entities.

Officials at the U.S. Conference of Catholic Bishops could not be reached for comment. Supporters of the Catholic hospitals, however, said that preserving health systems’ right to follow religious directives is critical to offering patients choices when it comes to their medical care.

Matt Bowman, senior counsel for Alliance Defending Freedom, a Christian legal organization, said the ACLU’s ultimate goal is to force Catholic hospitals to offer abortions against their faith. “The ACLU is trying to force religious hospitals and doctors to destroy babies in the womb, and it is trying to deprive women of the choice to go to a hospital that shares her faith and a doctor who shares her respect for human life,” said Bowman, whose organization represents three Christian and anti-abortion medical groups in Michigan that have sided with a Catholic health system there being sued by the ACLU.

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Federal law protects the right of hospitals and doctors to refrain from conducting abortions or sterilization procedures, Bowman said, and there is nothing new about doctors “living out their faith by healing the sick,” he said.

Lois Uttley, director of MergerWatch, said a Catholic hospital is the only option for many patients at a time when hospitals across the country are merging, being taken over and shuttering. “The two types of hospitals that have grown are Catholic-affiliated or for-profit. All other kinds are declining,” she said. “I do think that Catholic health care in general is very good. The problem is with the restrictions on reproductive health care.”

In 46 regions in the United States, according to the report, the federal government has labeled a Catholic institution the “sole community hospital.”

The bishops’ guidelines for health-care providers, a 43-page document, include many faith-based prohibitions for doctors. Sexual assault victims cannot receive any treatment that would destroy a fertilized egg or prevent it from implanting. Couples cannot receive sperm or egg donations from people other than their spouses. Abortion and sterilization are banned.

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The ACLU has in recent years taken several Catholic health systems to court, with mixed results.

In 2013, the organization sued the U.S. Conference of Catholic Bishops on behalf of a Michigan woman who went to her county hospital when she was 18 weeks pregnant because her water broke. Instead of terminating the pregnancy to avoid infection, the complaint alleged, Mercy Health Partners sent her home with painkillers in accordance with the Catholic directives. She later miscarried after contracting a severe infection, according to the ACLU.

A federal judge dismissed the suit on jurisdictional grounds, finding that it was inappropriate for the court to interfere in religious directives of this nature. The case is under appeal.

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Last year, the ACLU sued two of the nation’s largest Catholic health systems, Trinity Health in Michigan and Dignity Health in California, alleging that the health systems violated a federal law requiring hospitals to provide emergency care and discriminated against women. And earlier this year, it sued the federal government for allegedly allowing the bishops to deny critical health services to human trafficking victims. The ACLU was joined in its suit against Dignity Health by the California Medical Association, which represents 41,000 doctors.

This post has been updated.