James McAllister, a 56-year-old Lutheran minister in the midwest, was working on his sunday sermon one Thursday afternoon last summer. It wasn't going well. The reverend wasn't suffering from writer's block—in fact, he was crafting quite an elegant parable about "the importance of making our whole lives a prayer." No, the problem was bigger than that. The sermon skated around a private truth that McAllister could no longer deny.

McAllister has learned that you can tell inspirational stories, grounded in social justice and tolerance and peace, without having to bring God into the picture—and this sermon was a masterful case in point. A woman in his congregation had recently dropped everything to care for her cancer-stricken daughter, and that selfless commitment was sacred in its way. "You can see how I cook the books a little bit to make it easier to look in the mirror," he says of his sermons. "But there are times when I get that sort of empty feeling in my stomach, like I'm a fraud."

Months ago, McAllister, who is presented pseudonymously here, took his crisis to the bishop. He'd lost the faith, he explained, and he wanted out.

"Oh you're not quitting," she said, waving her hand dismissively. "You haven't lost your faith."

"Um, yeah I have," McAllister said. "This is for real."

The bishop shook her head. For the church elders, McAllister's revelations simply did not compute.

"They're either in complete denial," he says, "or they're completely comfortable with the idea that they have a pastor who's a fraud, as long as he puts asses in the seats."

McAllister took the issue up with his psychiatrist. "It emerged that she was a devout Christian herself," he says. "To her credit, she tried to be professional." Where she had once begun and ended their sessions with prayer, she stopped when he asked her to. "But I could see she was squirming. You know, she was sitting with a man of the cloth who had lost it. She had problems with that."

To be a clergyman struggling with God in modern times is to reside at the center of a great battle. At a time when the tension between faith and doubt arguably defines the distance between people more than does or race or even , the Doubting Priest bears witness for the defense and the prosecution. (Mother Teresa's grave doubt, as revealed last fall in her letters, means one of two things: Either the closest thing to a modern saint was a phony, or her trials actually make her religious life more meaningful, a poignant example of faith not as a certainty but as a required test that leads to a more profound commitment.) The spiritual struggles of ministers and priests and rabbis remind us that, amid encroaching fundamentalism, atheism is also on the rise. The neo-atheist movement is fueled by outspoken academics and intellectuals including Richard Dawkins, Christopher Hitchens, and others who bombard the airwaves and bestseller lists with their calls for deconversion. You can now send your kid to an atheist summer camp or get yourself certifiably "de-baptized." (Britain's national Secular Society offers the service: "Liberate yourself from the original mumbo jumbo that liberated you from the original sin you never had.") There are hundreds of college-campus groups devoted to secular humanism. The Atheist Alliance International reports "so many speaking requests that leaders of national atheist groups can't keep up."

Even amid the neo-atheist din, a clergy member's crisis of faith stands out. The natural order of things is upset when those entrusted with the protection of souls lose the plot. Because the clergy's livelihood and public are intimately bound up with their faith, practical considerations can be just as pressing as theological doubt. And the split between private beliefs and public sermons can leave religious leaders feeling deeply inauthentic, a source of psychic that most laypeople will never know.

Many soul-searching clergy never leave the church, making the ranks of ordained agnostics and atheists impossible to tally. But the raw numbers aren't much on the minds of clergy actually in the throes of deconversion. Their doubt is as real and immediate as a cloud over the sun. And somewhere in the nest of questions is a simple one: How did this happen?

McAllister had been raised Catholic, then drifted into a 25-year interregnum where he stopped going to church and called himself an atheist. A spiritual restlessness nudged him into chaplaincy training years ago. A second- minister—for most of his life he was a graphic designer and a fine artist—McAllister approaches the Big Questions more in the manner of a scholar than of a monk. (Even as a Catholic grade-school kid, he recalls, he hungered for real evidence. "Why," he would ask the nuns, "did this stuff all happen so long ago before there were cameras and TVs? Why aren't there prophets and holy people and miracles now?") Frustrated with his denomination but by no means ready to bail out, he picked up Sam Harris's book The End of Faith. He found he "agreed with about 98 percent of it."

He picked up other books in the neo-atheist canon. He read Richard Dawkins's The God Delusion, and then the one-two punch of Christopher Hitchens's mega-bestselling God Is Not Great and Sam Harris's Letter to a Christian Nation. He closed the latter book and found himself saying, aloud, "Amen." He had to face his misgivings. "I realized, it isn't just that I'm hurt by the way I was treated at synod, and it isn't just that the senior pastor that I work with was an asshole. It's that I don't believe in this anymore. And that was terrifying."

McAllister is not just scared for himself. "I know that my parishioners look to me for comfort," he says. "They're coming to the end of their life and they want some assurance that it's all going to be OK. I have sat at the deathbed of people in my congregation and told them what I regard as lies—or , at least—just to give them comfort. I'm willing to do that up to a point, but not for the rest of my working life."

Then there's the practical dimension. McAllister owes the church $18,000 for his schooling, at the same time as he's trying to put his last son through college. "I'm 56, which isn't a real good age to be pounding the pavement, and I've got a master's of divinity, not the most marketable degree in the world."

Richard Dawkins is convinced that McAllister's situation is common; in fact, he hopes one day to address it through "clergyman-retraining scholarships," set up through his charitable foundation, to "bridge the gap between living a lie and getting a new life," as he puts it.

McAllister's dilemma is familiar to Dan Barker, who coheads the Madison, Wisconsin-based Freedom From Religion Foundation (FFRF). The group spreads the word about atheism and fights legal battles to keep church and state separate. It is a soft place to land for the doubters who find it. Barker daily receives e-mails and letters from people who are wrestling with issues of faith, and he always writes back promptly and cheerily. E-mails from clergy are a very small part of the mix. But of all the stories he hears, these are the ones that resonate most—because they are his story, too.

Barker was a religious prodigy. Raised attending a Pentecostal church near Disneyland, he received "the call" at age 15, and wasted no time spreading the good news. He converted his high-school Spanish teacher. He became part of an evangelical team that went door-to-door holding revival meetings. He penned and performed popular Christian jingles.

But after a milestone birthday, number 30, came and went in 1979, Barker found himself agitated. Creatively, he was stalled; he was having trouble working on a Christian musical about a lost lamb, "because," he explains, "my views were changing while I was trying to write it." The restlessness, he determined, was spiritual. "It was as if there was a little knock on my skull and somebody was saying, 'Hello! Anybody home?' I was starving and didn't know it, like when you work hard on a project and forget to eat and don't know you are hungry until you are really hungry."

He began reading widely outside the Christian canon: science magazines, psychology, . It was the liberal-arts he never had, and what followed was "a slow but steady migration across the theological spectrum" that took about five years. (Among the deeply faithful, doubt is often first stoked with exposure to the "outside world.")

As he carried on a secret life of secular reading, Barker phased out the fire-and-brimstone sermons. "But even then I felt hypocritical, often hearing myself mouth words about which I was no longer sure, but words that the audience wanted to hear."

The confirmation, as Barker interpreted it, came one night in November, as he lay on a burlap cot in a church in a Mexican border town where he'd come to give a guest sermon. As he peered out at a splash of stars, Barker had a sudden profound sensation that had nothing to do with intellect, the kind of deeply felt moment more commonly associated with finding God than losing Him. He was, Barker understood, utterly alone here.

"For my whole life there had been this giant eyeball looking at me, this god, this holy spirit, this church history, and this Bible. And not only everything I did but everything I thought was being judged: Was God pleased? I realized that that wasn't there anymore. It occurred to me, 'I own these thoughts. Nobody knows what I'm thinking right now. There's no of hell, no fear of judgment, I don't have to be right or wrong, I can just be me.'" It felt as if charges had been dropped for a for which he had been falsely accused. It was exhilarating and frightening all at once. "When you're ready to jump out of an airplane to skydive, you can be terrified but excited at the same time," he says. "There's a point where you go, all right, let's do this."

Says Barker: "we surveyed our members some years ago, asking them: "If you were raised religious, why did you change your mind?" There was no one answer. Some people gave social reasons: the way the church treats women. Some people gave reasons like, 'the fear of hell—I just couldn't live with that.' But the answer people gave more often than any other was that it was intellectual: Religion eventually just did not make sense."

Looking back, Tom Reed, a former Roman Catholic priest from Mississippi, can pretty clearly identify his own moment of truth. It followed a quick succession of historical events: the 1968 Vatican statement upholding opposition to birth control and the death of Martin Luther King Jr. The two events finished off Reed's faith in the church and his faith in God.

For Reed, deconversion was almost as quick and binary as the flick of a switch. At a certain point, he says, "it was suddenly clear that the courageous thing to do was to just admit that this is all made up.

"I remember waking up one day saying, I'm going to practice being an atheist, just move through the day with that in mind. It had become a part of my being, the idea that God was ultimately responsible for everything that was happening. Now I proceeded from the assumption that there was no God in the picture."

It sounds like a coolly rational process, a Jesuitical internal debate tipping forward into certainty. It wasn't. "It was scary as hell," Reed says. "I realized, 'I'm not going to see my mother and father again.' " The sense of cold finality, the impression that one's prayers are just so many tennis balls served into the ocean: Such existential issues are a big part of anybody's crisis of faith. But for religious leaders, the stakes are raised even further, for faith is no longer a private matter.

"As a clergyman your livelihood is not just a job—it's a whole theological system that you'd better be on board with," says Dick Hewetson, a former Episcopal minister from Minnesota who left the church to do secular work and soon called himself an atheist.

"It hit me during those last couple of years in the pulpit that everything coming out of my mouth was being taken as gospel," he says. "I began to think, This is crazy. If I tell these people something, they believe me. Remember Jonestown? People asked, How could that happen? Well, I know how. I wasn't the Jim Jones type, and my people weren't the Jonestown type. But I was the shepherd and they were the sheep, for sure."

Charles Templeton, the late Canadian evangelist-turned-journalist, argued that a disjunction between what clergymen say publicly and what they believe privately is so common that serious comes with the territory. "Most intelligent clergymen preach to the right of their theology," Templeton wrote in his memoir Farewell to God. "They are more conservative in the pulpit than they are in private conversation or when a parishioner."

What eventually happens, as it did for James McAllister, is that sermons become cooler and less dogmatic. The clergyman, stated Templeton, "is likely to settle for what might best be described as an , do-goodest Christian philosophy."

Krista Wren [name changed], who never became a minister only because doors were quietly closed in front of her, tells a tale of spiritual disaffection with an ironic twist. A minister's wife from Atlanta and "a flailing Christian for 23 years," Wren worked with her husband on Pat Robertson's ministry before leaving to do missionary work in Africa. She thought of herself as a missionary; unfortunately for her, no one else did. At one fund-raising meeting prior to the couple's African departure, three dozen people gathered around her husband, Tom [name changed], and one said a prayer: "God, anoint Tom to bring forth your word with power! Let him see miracles as he prays for the people of Africa. May he lead many to Christ as you empower his words... " Then the crowd gathered around her. She held her breath in anticipation. "And Dear God," a woman's voice said, "please give Krista creative ways to do laundry." It was a decisive moment and in a way a portent of the end. "Maybe I've not gotten past it because it sums up the mind of many churches and even so many scriptures," Wren wrote in a recent e-mail to Dan Barker, with whom she had been corresponding. "Men do great things for God—and women wash their shorts."

Wren is currently a hairsbreadth away from throwing it all over the side and coming out as an atheist.

But here is the twist: Her husband became a pastor only because, many years ago, she converted him. ("And with a great deal of effort.") Now she's heading back across the bridge the other way. She is virtually certain he won't make the trip with her. What is certain is that their will be tested. Her disaffection is a subject so delicate she handles it with tongs.

"I'm hesitant to say too much, but the things that I have said have caused him to look as though his dog just died. When he learned I was corresponding with Dan—he looked over my shoulder in the middle of an e-mail—the color drained from his face. He shook his head and said, as he walked out of the room, 'This is just sad.' Well, part of me thinks it's sad, and part of me thinks it's about damn time."

Barker's own marriage did not survive his spiritual U-turn. (His wife, who remains faithful, remarried a Baptist minister.) And their four children?

"We both agreed that the children should never have to be in a position where they had to choose sides." One son has announced that he doesn't believe in God. One daughter "was going to a Unitarian church for a while, and I think she might be a nominal believer." A second daughter "has been a New Agey believer for a while." The third daughter is patently, traditionally religious. Barker seems pleased by the way the kids landed all across the spectrum of belief/disbelief, pixels in a snapshot of . Religious conversion is often explained in part as an effort to relieve the tension of uncertainty ("If the decision could be made conscious," psychiatrist M. Scott Peck once wrote, "I think it would be as if that person said to himself or herself, 'I am willing to do anything—anything—in order to liberate myself from this chaos.'") But letting faith go, in the end, can bring relief, too.

"We tend to ignore how much cognitive effort is required to maintain extreme religious beliefs, which have no supporting evidence whatsoever," says the evolutionary biologist David Sloan Wilson. He likens the process to a cell trying to maintain its osmotic pressure. "You're trying to pump out the mainstream influences all the time. You're trying to maintain this wall, and keep your beliefs inside, and all these other beliefs outside. That's hard work." In some ways, then, at least for fundamentalists, "growing out of it is the easiest thing in the world."

In Dan Barker's journey from fundamentalism to atheism, there were two stages of disillusionment. First came the loss of faith in the religion (that is, the loss of faith in the literal word), and then came the loss of faith in faith itself.

"The first step is hardest," he says. "Because as a fundamentalist, there is no middle ground.

"I remember a pastor telling me that he had a couple of congregants who didn't believe in the historical truth of Adam and Eve. They thought that Adam and Eve were a metaphor. I was shocked. I thought, 'How can you even let them be in your church? If parts of the Bible can be allegorized, then anything goes!'

"But I made the leap: OK, the fact that I disagree with these Christians should not be grounds for disfellowshipping them. That was a hard thing for me to do. But once I did it, the later flying leaps that I made were easier to take, psychologically, because I'd already admitted some gray."

A number of the clergy who have contacted Barker tell of a similar spiritual arc. It's as if a kind of psychological algorithm begins to work, with the shedding of illusions proceeding in inevitable, sequential steps, until an outdated belief is pitched with last night's coffee grounds. We wake up, if we're lucky: case closed.

And yet it is not so simple as that. Carlton Pearson is an example of a clergyman whose spiritual about-face need not end up where neo-atheists say it should. In the 1980s and early 1990s, Pearson, then a Pentecostal bishop, was among the most prominent and beloved fundamentalist preachers in the American South, heading up a megachurch in Tulsa, Oklahoma, with a loyal congregation 5,000 strong.

But something happened to Pearson as he and his church nosed toward the millennium. He stopped believing in hell and sin and the literal interpretation of the scriptures.

He was eating dinner in front of the TV with his baby daughter. On the news, Peter Jennings was revisiting Rwanda, investigating the fallout from that country's civil war. The scene was nightmarish: tiny infants, flies in their eyes and hair red from malnutrition groping at the empty breasts of their skeletal mothers. Carlton looked over at his own plump-faced child, then back at the TV. These African kids would soon be gone. Gone where? According to his own formal belief system, they were bound for hell. Somebody, he thought, needs to preach the gospel to these kids right now. To save them.

And then another thought formed. "You think I'm sucking them into hell? Carlton, look. They're already there." This, he thought, is where the pain comes from, all the weeping and wailing and gnashing of teeth. We do it to each other, and to ourselves. "I saw emergency rooms and courts and jails," Pearson recalls. "For the first time in my life, I did not see God as the inventor of hell."

It was a very different Carlton Pearson who returned to the pulpit. A lot of things he had been preaching, he told his congregation, were wrong. The central premise of their faith, the idea, "as my dad used to put it, that 'You gonna be cookin,' but you ain't never gonna get done!' " was bogus. There is no eternal damnation.

Almost all of the flock abandoned Pearson, who was officially declared a heretic by the College of Pentecostal Bishops.

Like Dan Barker, Carlton Pearson made a big leap away from literalism. And that leap set a chain-reaction of new perceptions: He became much less judgmental, more receptive to people and ideas he had dismissed or discounted. Unlike Barker's leap, Pearson's did not land him in a godless place. Throughout his trials the transmission signal of the divine, a felt thing, an inarticulable but absolutely bet-the-farm certainty persisted.

And so instead of abandoning God he invented a new theology that he calls the "gospel of inclusion," and he hung out a new shingle for a church he calls New Dimensions. It's a theology that gives everyone, not just avowed Christians, hope of salvation—and spares everyone the eternal fire of hell.

"I believe the logic of God is inerrant," he says. "I don't believe that the letter is. The logic of God would be love; the letter of God would be law." That Pearson is nominally a Christian seems almost a trivial point. After he was officially declared a heretic by the College of Pentecostal Bishops, the Unitarian Church of Christ opened its arms to him; and since it preached an inclusiveness he appreciated, the denomination seemed as good a place as any to hang his hat.

The Unitarian Church is a haven for many an atheist and agnostic, offering the comforting ritual (hymns are often rewritten with nontheistic lyrics) and esprit de corps of religion, without the dogma. Suzanne Paul, a minister to the New Hope Unitarian Universalist congregation in the suburbs of Detroit, was raised Roman Catholic, but could not stop questioning the "logic" of the Bible, and concluded that she was an atheist at age 20. She became involved in Judaism through her husband and finally found a niche in New Hope, where she leads holiday celebrations she sorely missed. "We celebrate Passover, Easter, Yom Kippur, asking, 'What can we learn from this holiday?' Yom Kippur, for example, is about and atonement. We are naturally social animals and like to be with like-minded people. I enjoy the community aspect of religion but not the theistic end of it."

It took Suzanne some three decades to openly declare herself an atheist. "I recognized early that you can clear a room if you say you're an atheist. I prefer to identify myself as a humanist."

Pearson, too, has struggled with when and how to characterize his beliefs. "I don't always say this publicly but I'm starting to feel more free to do so: I don't necessarily believe in a god, or the God; I just believe in God."

Since his new direction, Pearson's fortunes have plummeted. Only about a hundred people hear him preach on Sundays at 1 p.m. because they have to wait until the Episcopalians finish their service. "We're in a foster-care program," he says.

And when people approach him and say, "Bishop Pearson, I'm losing my faith," he now has a better answer.

"We spend our lives impersonating who we think others want us to be," he says. "And we end up as living impostors. So, when someone comes to me and tells me they're losing their faith, I congratulate them. You're starting to embrace your own thinking self—the essential, immutable, immortal self— as opposed to the accidental criminal you have been made to think you are."

Doubt, for Carlton Pearson, isn't a sign that one's faith is evaporating; it's just a sign that it's going underground and changing.

And so there emerges, in the literature of spiritual self-transformation, a kind of parallel canon between the religious conversions and the Dawkins-style deconversions. It is the idea of the full circle, or the nun-turned-religious scholar Karen Armstrong's so-called "spiral staircase," wherein we eventually come back around to our old spiritual position, but at a higher level, from which we see a wider landscape.

It's the story of the young . Growing up in Geneva, he watched his parson father become tormented by religious doubt. This made him reject conventional religious practice, but it sharpened his sense of the importance of some sort of personal spiritual quest, which he regarded as the main issue in the life of everyone over 35.

The desertion of priests and nuns from the Catholic church since the 1960s seems to be the story of an en masse loss of faith. "But it can also be seen as a strengthening of faith," says John Portmann, a professor of religious studies at the University of Virginia, who is working on a book on "cultural Catholicism." (By far the most-cited reason for leaving was unrelated to God: It was church policy on celibacy and marriage.) "If some semblance of faith can persist in spite of all [the church's missteps and scandals], you know your faith is real, you weren't in it for the trappings of the church or the comfort of the rituals."

Dan Barker has now been an atheist longer than he was a believer, and he is at peace with his decision. But for the more recent deconverts, some struggles remain. Perhaps chief among them is finding a substitute for the very real consolations that faith provided. When you've lost God, how do you fill the void?

"That's what I'm wrestling with now," says James McAllister. "I don't have anyone to talk to in my heart. The prayers I used to say, I simply don't bother anymore. I obviously regard prayer to be silly, even. But it was a comforting place that I could go. I've let that go. And there is a void. And hopefully it can be replaced just by appreciating being alive."