"We don't know anything about Hillary in terms of religion," he said, speaking to a group of Christian leaders in New York. "Now, she's been in the public eye for years and years, and yet there's no -- there's nothing out there. There's like nothing out there. It's going to be an extension of Obama but it's going to be worse, because with Obama you had your guard up. With Hillary you don't, and it's going to be worse."
Trump was addressing a small group of high-profile evangelicals ahead of speaking before a larger group of religious leaders at a gathering hosted by the Christian group, United in Purpose.
E.W. Jackson, who tweeted video of Trump's remarks, said the comment came while Trump was trying to say that conservatives tend to get questioned more about their faith than liberals.
"I think everybody in there knows Hillary Clinton is a Methodist and by definition a Christian," Jackson told CNN. "He was saying for those of us who are students of the Christian faith -- for evangelicals that can mean everything is thoroughly examined, like what do you believe about marriage? What do you believe about abortion?"
Jackson, who ran as the 2013 Republican nominee for lieutenant governor in Virginia, said he was "accused of believing all kinds of crazy things" when he was a politician.
"All (Trump) was saying was she hasn't had that same examination, so we don't really know what she believes," he added.
Ken Blackwell, a Family Research Council fellow and Ohio politician, praised Trump's comments about "protecting religious liberty and speech, because I know this administration -- and given that the Hillary administration will be a third term of Barack Obama, she would be a third term in her attack on religious liberty in general."
"I have no reason to attack her faith, I just question her ability to defend my right, my family's right, my church's right to practice our faith in the public square," Blackwell said.
Marjorie Dannenfelser, the president of the Susan B. Anthony List, said there's been "very little public conversation about (Clinton's) faith."
"I think it would be very helpful to hear what her faith is, what the core of her belief is," she said.
The day after Trump's remarks, Clinton appealed to her Christian faith as the guiding source for her desire to help children.
"Every single child deserves the chance to live up to his or her God-given potential. That has been the cause of my life. It's rooted in the values that I've learned from my family and my faith," she said Wednesday in Raleigh.
"We have responsibility to lift each other up," she added. "As we Methodists like to say, do all the good you can to all the people you can in all the ways you can."
While it's true Clinton doesn't regularly talk about her faith, she has had a number of public interactions with people where they discussed her faith.
She also talked about her faith in an interview with CNN in January, saying, "My faith is a central part of who I am."
"What I believe, why I'm called to service because I feel that I've had a lot of blessings in my life and a lot of others are not so fortunate," she said. "And I'm grateful that I was both raised with a faith and that the faith has sustained me. I am very committed to what I believe is the discipline and the mandates that you should be responding to as a Christian and for me that has a lot to do with, you know, lifting up those who are the last, the lost and the least among us and trying to give more people a chance to chart a more positive for themselves. That's what I've always cared about and that's what I'll do as president."
Trump has questioned other candidates' faith, as well. Of Texas Sen. Ted Cruz, Trump tweeted in February: "How can Ted Cruz be an Evangelical Christian when he lies so much and is so dishonest?"
He also urged the group Tuesday to pray for his election.
"What you really have to do is pray to get everybody out to vote, for one specific person," Trump said. "And we can't be -- again -- politically correct and say we pray for all of our leaders because all of your leaders are selling Christianity down the tube, selling Evangelicals down the tubes."