The lawsuit concerns a rule that went into effect in July clarifying an anti-bias provision of the Affordable Care Act, otherwise known as Obamacare. The health law prohibits discrimination in certain health programs that receive federal funding. While it does not explicitly apply to transgender people, the rule issued by the Health and Human Services Department specifies that it considers discrimination on the basis of gender identity a form of sex discrimination, as other agencies and many courts have done.

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This is not the first time the Obama administration has come under fire for strengthening protections for transgender people. In May, the Education Department directed public schools to allow students to use the bathroom that matched their gender identity. The directive was blocked after 13 states sued, saying it was improperly issued. The question of how schools must accommodate transgender students will be considered by the Supreme Court later this year in a case brought by a high school student from Virginia barred by his school district from using the boys’ restroom.

Gay and transgender rights groups said the health rule offers critical protections for transgender people because they often struggle to receive appropriate care from physicians and hospitals.

“What the rule says is if you provide a particular service to anybody, you can’t refuse to provide it to anyone,” said Sarah Warbelow, the legal director for the Human Rights Campaign. That means a transgender person who shows up at an emergency room with something as basic as a twisted ankle cannot be denied care, as sometimes happens, Warbelow said. That also means if a doctor provides breast reconstruction surgery or hormone therapy, those services cannot be denied to transgender patients seeking them for gender dysphoria, she said.

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But the Catholic groups contend that the rule forces doctors to provide services that may conflict with their religious beliefs or professional judgment. Douglas Wilson, chief executive of the Catholic Benefits Association, said in a statement that Catholic hospitals already care for patients in a way that does not discriminate.

“Catholic hospitals provide compassionate care to everyone, regardless of status. Patients experiencing gender dysphoria deserve no less,” said Wilson, whose group includes 880 Catholic hospitals, colleges and businesses. “The prime ethic of any healthcare provider is do no harm. These regulations do the opposite.”

The groups also allege the rule will force doctors and hospitals to perform abortions against their faith.

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Several states and some other Catholic organizations had already filed suit over the rule on the grounds that it undermines religious freedom.