They are reeling not only from the loss of the presidency, but from what many of them see as a rejection of their agenda. They lost fights against same-sex marriage in all four states where it was on the ballot, and saw anti-abortion-rights Senate candidates defeated and two states vote to legalize marijuana for recreational use.

It is not as though they did not put up a fight; they went all out as never before: The Rev. Billy Graham dropped any pretense of nonpartisanship and all but endorsed Mitt Romney for president. Roman Catholic bishops denounced President Obama’s policies as a threat to life, religious liberty and the traditional nuclear family. Ralph Reed’s Faith and Freedom Coalition distributed more voter guides in churches and contacted more homes by mail and phone than ever before.

“Millions of American evangelicals are absolutely shocked by not just the presidential election, but by the entire avalanche of results that came in,” R. Albert Mohler Jr., president of the Southern Baptist Theological Seminary, in Louisville, Ky., said in an interview. “It’s not that our message — we think abortion is wrong, we think same-sex marriage is wrong — didn’t get out. It did get out.

“It’s that the entire moral landscape has changed,” he said. “An increasingly secularized America understands our positions, and has rejected them.”

Conservative Christian leaders said that they would intensify their efforts to make their case, but were just beginning to discuss how to proceed. “We’re not going away, we just need to recalibrate,” said Bob Vander Plaats, president and chief executive of The Family Leader, an evangelical organization in Iowa.

The election results are just one indication of larger trends in American religion that Christian conservatives are still digesting, political analysts say. Americans who have no religious affiliation — pollsters call them the “nones” — are now about one-fifth of the population over all, according to a study released last month by the Pew Forum on Religion and Public Life.

The younger generation is even less religious: about one-third of Americans ages 18 to 22 say they are either atheists, agnostics or nothing in particular. Americans who are secular are far more likely to vote for liberal candidates and for same-sex marriage. Seventy percent of those who said they had no religion voted for Mr. Obama, according to exit polls conducted by Edison Research.