But it's far from clear whether the greater political problem is Kerry's or the church's. "I don't think it complicates things at all," Kerry told TIME in an interview aboard his campaign plane on Saturday, the first in which he has discussed his faith extensively. "We have a separation of church and state in this country. As John Kennedy said very clearly, I will be a President who happens to be Catholic, not a Catholic President." Still, when Kennedy ran for President in 1960, a candidate could go through an entire campaign without ever having to declare his position on abortion—much less stem cells, cloning or gay marriage. It was before Roe v. Wade, bioethics, school vouchers, gay rights and a host of other social issues became the ideological fault lines that divide the two political parties and also divide some Catholics from their church.

Kerry is a former altar boy who complains when his campaign staff does not leave time in his Sunday schedule for Mass, who takes Communion and describes himself as a "believing and practicing Catholic, married to another believing and practicing Catholic." But just last week he made a rare appearance on the Senate floor to vote against a bill that would make harming a fetus a separate offense during the commission of a crime. The vote put Kerry on the same side as abortion-rights advocates in opposing specific legal rights for the unborn—and against nearly two-thirds of his fellow Senators.

Polls consistently show that Americans prefer their leaders to be religious, and in running to unseat the most openly devout President in recent years, Kerry has at times put a pious cast on his own rhetoric. In a speech at a Mississippi church on March 7, he said Bush does not practice the "compassionate conservatism" he preaches, and quoted James 2: 14, "What good is it, my brothers, if a man claims to have faith but has no deeds?"

Kerry says his faith was instilled in him in childhood and that in Vietnam he wore a rosary around his neck when he went into battle. When Kerry got home from the war, he went through what he calls a "period of a little bit of anger and agnosticism, but subsequently, I did a lot of reading and a lot of thinking and really came to understand how all those terrible things fit." He is enough of a stickler for Catholic rules to have sought an annulment of his 18-year first marriage before marrying again. The Boston Globe's revelation last year that his paternal grandparents were born Jewish and converted to Catholicism has triggered "some fascination," he says, and some frustration over not knowing more about his religious heritage. "I wish my parents were alive and I could ask them all the questions," he says.

Kerry and other Catholic politicians have long argued that their religious beliefs need not influence their actions as elected representatives. That position is what provoked New York's Archbishop John Cardinal O'Connor in 1984 to castigate New York Governor Mario Cuomo and Democratic vice presidential nominee Geraldine Ferraro, who are both pro-choice.

If anything, the church is getting tougher. The Vatican issued last year a "doctrinal note" warning Catholic lawmakers that they have a "grave and clear obligation to oppose any law that attacks human life. For them, as for every Catholic, it is impossible to promote such laws or to vote for them." When Kerry campaigned in Missouri in February, St. Louis Archbishop Raymond Burke publicly warned him "not to present himself for Communion"—an ostracism that Canon Law 915 reserves for "those who obstinately persist in manifest grave sin." Kerry was scheduled to be in St. Louis last Sunday, and told TIME, "I certainly intend to take Communion and continue to go to Mass as a Catholic."

But, inevitably, his religion and his politics will clash. Already, one employee of the U.S. Conference of Catholic Bishops in Washington says he has lost his job as a result of his political activities on Kerry's behalf. Ono Ekeh was a program coordinator for the conference until last month, when he says his supervisors there confronted him with what he had written—sometimes using workplace computers—on his Yahoo discussion-group website, Catholics for Kerry. What alerted them to his postings, he believes, was a mass e-mail by activist Deal Hudson, editor of a Catholic magazine, Crisis, and a close ally of the Bush White House. Ekeh, 33, had criticized the bishops' recent edicts that Catholic politicians should vote according to church teaching.

How might the rift between Kerry and the church he calls a "bedrock of values, of sureness about who I am" affect the election? Catholics are among the narrow slice of the electorate considered truly up for grabs this year, and they constitute a major share of the voters in the Midwestern and Southwestern swing states. Those who are most strongly antiabortion are probably already in Bush's camp. But many Catholics are, like Kerry, struggling with contradictions between the church's teachings and what they practice. Still others say abortion is not the only issue that matters when they vote. "There are literally millions of American Catholics who struggle with different feelings and different issues at different times," Kerry says. In the Democratic primaries, Kerry ran particularly strong among Catholics—winning significantly larger shares of their votes in states like New Hampshire, Missouri and Tennessee than he received from Protestants.

Most Catholic officials expect that the church's response to Kerry's candidacy will vary from diocese to diocese. You may not see many Catholic bishops appearing at Kerry photo ops this campaign season, and there's a possibility of some uncomfortable moments on the trail. "All you need is a picture of Kerry going up to the Communion rail and being denied, and you've got a story that'll last for weeks," says Father Thomas Reese, editor of the Jesuit magazine America.

For now, theologians say, Kerry's conduct is principally a matter between the candidate and his own Archbishop. Boston Archbishop Sean O'Malley has given him Communion in the past; the Senator took the sacrament at O'Malley's installation last July. More recently, however, O'Malley has said that Catholic politicians who do not vote in line with church teachings "shouldn't dare come to Communion." But between the gay-marriage debate in Massachusetts and his efforts to repair the damage from the sexual-abuse scandal that began in his archdiocese, O'Malley already has a plateful of controversy. Kerry, for his part, is planning to avoid stirring any up. "I don't tell church officials what to do," he says, "and church officials shouldn't tell American politicians what to do in the context of our public life."