Judge Paul Engelmayer said Wednesday that the rule was unconstitutional, arbitrary and capricious. He said the rule would have led to some patients facing discrimination because hospitals and clinics that did not comply with it would lose federal dollars.
Critics saidgay and transgender patients were particularly at risk of being denied care.
The rule was to have taken effect this month, but 23 states and cities along with Planned Parenthood and other health care providers sued to stop it.
A spokeswoman for the Health and Human Services Department said it was studying the judges ruling and would not comment.
The rule spun out of President Donald Trumps promise to expand religious liberty protections under federal law.
In May, HHS published what it called30 conscience provisions that health care providers hadto comply with if they wanted to receive federal funds.
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