AILSA CHANG, HOST:

Religious freedom has been a major focus of the Department of Health and Human Services under the Trump administration. Today there was a major blow to those efforts. A federal judge in Manhattan has thrown out a rule from HHS designed to protect the so-called conscience rights of health care workers.

Here to explain is NPR health policy reporter Selena Simmons-Duffin. Hey, Selena.

SELENA SIMMONS-DUFFIN, BYLINE: Hi.

CHANG: So can you just first explain, what are conscience rights? What does that even mean?

SIMMONS-DUFFIN: Right. So this relates to the HHS Office for Civil Rights, and that's an office that receives complaints in three different categories. The biggest is patient privacy, like HIPAA. It also receives complaints of civil rights violations.

And then this last court category is conscience rights. So what that means is a doctor or a nurse who has religious objections to certain procedures or services - commonly, we talk about abortion, care for transgender patients, assisted suicide - if a doctor or nurse like that is forced to participate in that kind of care, they can file a complaint that their conscience rights have been violated to the Office for Civil Rights. And the director of that office is Roger Severino. He has made clear since he came in that religious freedom and conscience rights is his priority in that role, and that's the context for this rule.

CHANG: OK. That's the context. So when the rule came out in May, what did this rule do?

SIMMONS-DUFFIN: So the things that it did is it expanded who could file that type of a complaint that I just described to billing staff, scheduling staff. A doctor or nurse or this other kind of health worker did not have to give their employer prior notice that they objected to give this kind of care. There were no exceptions for medical emergencies. If a hospital, for instance, was found to have violated a health care worker's conscience rights, HHS could have taken away all of its federal funding.

CHANG: Wow.

SIMMONS-DUFFIN: Yeah. So...

CHANG: It's a large consequence.

SIMMONS-DUFFIN: Yeah, really big consequences. So part of the justification for issuing this rule is the office said that there was this big unmet need, that providers of faith were being forced to do things all over the country. Historically, there's only been one of these kind of complaints that's come into the office every year. That's been for the last 10 years or so.

CHANG: OK.

SIMMONS-DUFFIN: But Severino keeps on saying that that number of complaints has just shot up. And he said last year, the office got 343 complaints.

CHANG: Wow, that's quite an ascent. But after this rule came out, wasn't it immediately challenged in court?

SIMMONS-DUFFIN: Yes. It was - the HHS was sued right away in this case by Planned Parenthood, the state of New York, lots of other states and cities and organizations. And today, what happened is the U.S. District Court Judge Paul Engelmayer of the Southern District of New York vacated the rule. He found the rule's violations of federal law were, quote, "numerous, fundamental and far-reaching." And he also found that HHS exaggerated the need for this rule. So remember I was just talking about 343 complaints.

CHANG: Right, the number of claims that came in last year. What about them?

SIMMONS-DUFFIN: Right. So apparently, that's an - a made-up number. The government submitted...

CHANG: Really?

SIMMONS-DUFFIN: ...These complaints.

CHANG: OK.

SIMMONS-DUFFIN: And the court analyzed them and says, instead of 343, the real number is 20. A government lawyer said on the record that that is the ballpark for the complaints that have come into the office. So the judge called that admission fatal to HHS's justification.

CHANG: Three hundred forty-three versus 20 - that's quite a discrepancy.

SIMMONS-DUFFIN: Yes.

CHANG: OK. So what's next in the litigation?

SIMMONS-DUFFIN: So there is weirdly another case against this rule in another district court. This one is in the Northern District of California. A ruling is expected there, but it's not clear what happens now that the rule's been vacated. I asked HHS what's next, and it would not comment on a possible appeal - only said that it was reviewing this court's opinion.

CHANG: That's NPR's Selena Simmons-Duffin. Thanks, Selena.

SIMMONS-DUFFIN: Thank you.

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