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"I find it deeply disturbing that we are going in that direction," Clinton told attendees of the Aspen Ideas Festival in Colorado when asked about the decision.
In its 5-4 ruling, the Supreme Court found that certain, smaller employers, including the Hobby Lobby arts and crafts chain, could earn an exemption from the mandate by claiming religious opposition.
However, Clinton, a former attorney, was unswayed.
"It is very troubling that a salesclerk at Hobby Lobby who needs contraception - which is pretty expensive - is not going to get that service through her employer's healthcare plan because her employer doesn't think she should be using contraception," she continued. "This kind of decision raises serious questions."
Clinton also argued some businesses will lie about their owners' religious beliefs in order to avoid providing services to women.
"I think there should be a real outcry against this kind of decision," she said. "Many more companies will claim religious beliefs and some will be sincere, but others maybe not. And we're going to see this one insurable service cut out from many, many women."
She went on to cite the possibility of employers claiming they are religiously opposed to blood transfusions and other medical procedures.
"And there's a lot of other things," Clinton said. "This is a really bad slippery slope."