At the adolescent-unfriendly hour of 7:10 on this rainy spring morning in tiny Loachapoka, Ala., classes won't start for another half hour in the public school. But already the science lab at Loachapoka High School is coming alive with the banter of 13 teens sloughing off backpacks and settling in to learn – not about chemistry or biology, but about faith.

"Who knows what happened this weekend?" asks Kevin Flannagan, regional director for Campus Life ministry.

Immediately, the teens quiet down to listen. "Easter," a boy volunteers.

"Jesus rose, yes," Mr. Flannagan says. Then, in a tone as gentle as it is friendly, he recaps the Bible story and asks, "So why is it called Good Friday?"

A girl answers: "Because he died for us, and that's a good thing." A few heads nod.

As Flannagan goes on to tell the story of a boy making an empty Easter egg – "he got it that the meaning of Easter is the empty tomb" – the emotional climate in the room is not one of fervor, but of comfort.

Asked why it's worth coming to school early for a Campus Life meeting, a lanky senior wearing an Adidas shirt answers simply: "I like to learn about Jesus."

It has been 50 years since the Supreme Court banned school-sponsored prayer. But God and faith are probably present in more ways now than ever in public schools, say law and religion experts and activists.

"We've gone from virtual silence about religion in the curriculum and virtually no student religious expression in many schools," says Charles Haynes, a scholar at the First Amendment Center and head of the Religious Freedom Education Project in Washington, D.C., "to today, when social studies and other standards are fairly generous to religion, and students are expressing their faiths in many different ways in many public schools, if not most."

Nobody has yet studied the phenomenon, but there are some illustrative examples:

• Student ministries that started before the school prayer ban, or just after, have expanded to reach tens of thousands of public school students. Since the mid-1960s, the Fellowship of Christian Athletes has established itself on more than 8,000 junior and high school campuses, many of them public. And Campus Crusade for Christ, founded in 1951 as a Christian ministry to college students in California and now known as Cru, has helped high school students start some 200 Christian clubs, almost all of them in public schools. Youth for Christ, an evangelical missionary organization in which broadcast-evangelist Billy Graham worked in the 1940s, began reaching out to high school and middle school students in the 1960s and '70s. It now has on- and off-campus clubs at 1,200 schools, most of them public.

• At the elementary school level, religious instruction sometimes takes place right on campus in after-school programs. By far the most widespread and controversial, Good News Clubs hold Sunday school-like classes in some 3,200 public elementary schools. After-school Good News Clubs have grown from fewer than 17,000 participants in 2001 to more than 156,000 enrolled in 2012.

• "See You at the Pole" began in Texas with 10 Christian students praying around their school flagpole in 1990. It has blossomed into a yearly ritual involving 1 million to 2 million public school students nationwide meeting on a designated September morning before class.

• Informal Bible study groups have proliferated, judging from anecdotal reports, sometimes meeting on campus, sometimes at a coffee shop or someone's home.

• Over the past 10 to 15 years, Muslim and Jewish student clubs as well as clubs espousing agnostic, humanist perspectives have appeared on public school campuses. Among the oldest, the Hindu Student Association of Bellaire High School in suburban Houston attracted 700 people of many faiths at its Holi celebration in April.

• Students in interfaith groups like Youth LEAD in Sharon, Mass., may meet off-campus, but stage workshops and programs at school.

• Students are also carving out time to pray, whether Muslims fulfilling a religious obligation or Christians delivering on prayer requests during lunchtime.

• Some schools allow released-time programs: During class hours, students leave campus for Christian, Jewish, Mormon, or Islamic instruction – some even earn academic credit.

• Schools are increasingly including Christianity, Buddhism, Sikhism, Islam, and, in some cases, the Bible in their curricula because of concern over Americans' religious illiteracy. (A 2007 study found that only 10 percent of American teens could name the five major religions.)

Many welcome the growing presence of religion.

"If the public school is to prepare people to participate in a democracy," says Mike Waggoner, editor of Religion & Education, "students are going to require an understanding of Hindus, Muslims, atheists, various forms of Christians, and so forth."

Mr. Haynes concurs, noting, "It is on public school campuses that young people learn to live with and address differences." But, he warns, if religion is going to come on campus, it has to enter "through the First Amendment door."

This means that public schools and their staffs cannot violate the Establishment Clause of the US Constitution by fostering religious beliefs. But neither can they stifle students' constitutionally protected freedom of speech and free exercise of religion.

Rulings that panicked school boards

So what exactly happened 50 years ago?

In two landmark decisions – Engel v. Vitale on June 25, 1962, and Abington School District v. Schempp on June 17, 1963 – the Supreme Court declared school-sponsored prayer and Bible readings unconstitutional. The rulings provoked unprecedented controversy, says Melissa Deckman, affiliated scholar with the Public Religion Research Institute in Washington, D.C. "School boards got so paranoid about dealing with religion that they just said, 'We shouldn't do any of that at all,' " she says.

Schools struck religion from curricula, teachers avoided the topic, and children got the message that religion took place off campus. But then, Professor Deckman explains, people began "to say, 'Look, religion is part of who we are and our culture.' "

Yes, the rulings restricted public school employees – but what about students? Could they say grace in the cafeteria or meet outside class to study the Bible, Quran, or Torah? Could religious organizations offer after-school programs? While teachers couldn't preach, could they address religion academically?

In court case after court case, the answer was a resounding "yes."

Granted, courts haven't always agreed. Reflecting regional attitudes, a court in Ohio deemed it legal for a student to wear a T-shirt sporting a Christian slogan critical of homosexuality while, in a similar case in California, a court ruled against the student. Similarly, says Charles J. Russo, who teaches law and theology at the University of Dayton in Ohio, US circuit courts have disagreed over the constitutionality of a student leading prayers at public school graduations. Federal courts in the West and Northeast ruled it illegal; courts in the South upheld it.

Supreme Court cases, however, hold sway nationwide, and two in particular fueled the growth of religion in public schools. In 1990, the court compelled public high schools to give student-led religious clubs the same access enjoyed by other non-curricular clubs. Then in 2001 the court ruled that elementary schools that welcomed programs such as Girl Scouts could not bar the after-school Good News Club because it was evangelical Christian. That violated the Free Speech Clause.

Rulings versus enforcement

Though the courts have consistently barred school-sponsored prayers, when Nicholas Weldy surveyed Ohio school superintendents for his University of Dayton doctoral thesis in 2001, more than 40 percent said there had been some form of prayer at graduation.

Some schools turn a blind eye to serve what they perceive as a greater good. At Hull Middle School in Benton Harbor, Mich., pastors walked the halls, broke up fights, and sat in the back of classrooms, their silent presence exuding authority.

"The kids had tremendous respect for them, probably more than for the police or the truancy officer," says Robert Lawrence, who taught at the school for 10 years before it closed in 2011. In this area, clobbered by unemployment, crime, and drugs, so many middle-schoolers had rap sheets that parole officers had a campus office.

Pastors occasionally addressed morning assembly and sometimes used Christian language in the hallways. But, Mr. Lawrence, who was not religious at the time, says, "I never saw a problem with it." The school population was predominantly African-American and culturally rooted in Christianity, so in his view there was no evangelizing: "It was an all-out war against the streets. Any help anyone could bring was more than welcome."

Similar "gray areas" arise involving religious clubs and programs. Briefly, clubs fall under the Equal Access Act, which stipulates that they must be student-led, participation must be voluntary, faculty sponsors can only observe, and no outside adult can "regularly attend." They can take place during the school day during a designated "club time" or after class.

Notasulga High School is an Alabama K-12 school west of Auburn with a turbulent history of desegregation. Today, 99 percent of its 405 students are eligible for the free lunch program, and despite a dramatic turnaround in graduation rates and test scores, principal Brelinda Sullen says she fights every day to keep the district from shutting the doors. When Campus Life director Flannagan asked Mrs. Sullen whether students would be interested in a program, she jumped at the opportunity: "It's all about character building, and Campus Life helps us build character in our kids."

But she knows the law, she says, and "I know how far I can go." She restricts attendance to high school students and makes it strictly voluntary. In the absence of other student clubs, anyone not participating can use club time for study hall. Though all high school students currently participate in Campus Life, Sullen says, a few students in the past have bowed out.

This suggests Campus Life is a religious club. But because Flannagan attends and conducts virtually every meeting, it could fall under rules for outside-led, after-school programs. As with Hull Middle School, the situation is not clear-cut and will remain so unless there is a complaint.

The religious 'huddle'

The Fellowship of Christian Athletes (FCA) is arguably the largest religious organization with a public school presence. Jeff Martin, executive vice president of ministry programs and resources, describes its "huddles" as student-led clubs with, ideally, coaches as faculty sponsors. A former college football player with a master's of divinity from Southwestern Baptist Theological Seminary in Fort Worth, Texas, he says the sponsors' influence is confined to a "ministry of presence, a ministry of attitude."

But anecdotal evidence suggests that policy can be one thing, implementation another.

When the huddle meets on Friday mornings at 6:30 at Peachtree Ridge High School in Suwanee, Ga., Alex Durham, a senior and FCA leader, is a stickler for the rules. The faculty sponsor "sits at the back," she says.

In other schools, however, the athletic department can be "somewhat semiautonomous," says Bruce Grelle, director of the Religion and Public Education Resource Center at California State University, Chico. When his students recall their high school days, he says, some note: "Oh, yeah, the coaches and the team, they always prayed together before the game." Some, he speculates, don't realize this is illegal while others "do realize it and say, 'Well, we're going to keep doing it this way until you want to make an issue of it.' "

A student athlete at Lakeside High School in Atlanta did just that a few years ago. A teacher scolded him for "being disrespectful" when he didn't bow his head in prayer at a team huddle, says Chaim Neiditch, a rabbi with the National Conference of Synagogue Youth. "The boy called me the next day."

The school website now says, "FCA was originally started by Christian athletes as a safe place where students could come meet with fellow Christians," but is now "very welcoming to all."

The website also now lists a Jewish Student Union that meets every other week before school with Mr. Neiditch, a guest as regular here as Flannagan is in Alabama schools. At a recent meeting, student leaders announced an ice-cream seder at Sara's house – "again!" – and begged their buddies to sing at a school-wide event. The 20-some students laugh; the faculty adviser smiles from her desk. Sometimes conversation turns to world events, and they ask Neiditch for the Israeli perspective.

This day, though, they dig into 30 pounds of challah dough. While the kids – most, not all, Jewish – roll and braid, the rabbi relates, locomotive-fast, the story of the Exodus, with the Red Sea parting and manna from heaven: "This reminds us that as we go through challenges God loves us and there is a reason for those challenges."

"You realize there's a lot more you can do to experience your Judaism," says sophomore Adam David. "It's scary here, so it's nice to have a small intimate group," he adds. He's referring to the fact that in Georgia, as Neiditch puts it, "everything is Gospel," whether spinning the dial on the radio, holiday shopping, or spotting church after church out the car window.

In Flushing, N.Y., a group of Christian students tried for years to meet at Townsend Harris High School, but the administration was adamant: no religious activity on campus. When a new principal took over, the group – the Seekers – tried again, asking assistant principal and fellow Christian Ellen Fee to be faculty sponsor. Some teachers worried that a religious club "would create a lot of 'us versus them,' " recalls Ms. Fee, who also teaches health and physical education. Others felt that "if kids are asking, then we have an obligation to them."

Today, Fee, who hosts a nondenominational church service in her home on weekends, is adviser to both the Seekers and the Muslim Student Association (MSA).

On two separate days, leaders of the MSA and Seekers agreed to meet with the Monitor. About half a dozen in each group gathered at a large table in Fee's office. Both clubs number 50 to 60 members, out of a student body of about 1,100. Some members are more religious than their parents; others don't have a youth group at their mosque or church. All, they say, feel it is key to have peers who share their school life and values. Besides providing a source of friendship, the clubs allow them to wrestle with how to live their faith where they spend most of their day.

The Muslim students, for example, talk about what it means for girls to wear head scarves – about half the MSA girls here do; the Christians struggle with how to evangelize without being obnoxious or coming across as superior. Both groups report discussing "sensitive issues" like dating pressures or views about homosexuality. These are the kinds of conversations Nabeel Hussain hankered for when he helped launch an MSA at Fishers High School in Fishers, Ind., last year. He wanted to make sure he could perform his prayers, but he also wanted the support of fellow Muslims to help him stay true to his faith in the face of pressures from peers and the culture at large.

Battling for students' souls

"I have no problem whatsoever if Muslims or Christians come together to practice their faith," says Melissa Thompson, a Christian and mother of a student at Blaine (Minn.) High School. "That is their right."

But Ms. Thompson wants the school to rein in members of the Christian club Catalyst. She says they've harassed her daughter with repeated, insistent invitations, even though she "had made it crystal clear for over a year that she had no interest in their group. They have an elaborate manual that tells them what their job is ... to go out and proselytize their peers."

Indeed, the group's manuals – available on-line at campusmovement.org, a coalition of Catalyst clubs – preach in hip, lower-case language that "taking the message of Jesus to the world around you isn't a hobby. it's a LIFE style. that's because it's not the great suggestion. it's the great commission ... there are so many opportunities in public schools to represent Jesus. don't be ashamed. if Jesus doesn't reject you, no one can."

Other organizations' materials and websites get downright militaristic. References to public schools as "a target" or "battlefield" are not uncommon. One website tells of the need "to be warriors in an eternal battle for the souls of these children and their parents," while a 2002 National Network of Youth Ministries (NNYM) manual states that Christian students "have been sent to establish a strategic beachhead so that they can penetrate and saturate the entire school with the good news of Jesus Christ."

Some NNYM leaders now counsel a far less aggressive approach, but the manual lives on and Thompson sees many parallels between its call to arms and Catalyst's actions at Blaine.

Thompson says she believes that a local youth pastor, who contributed to the 2002 manual, directs Catalyst members from afar, thereby violating the Equal Access Act. Though the Anoka-Hennepin School District did not side with Thompson, she is determined to fight on.

The controversy surrounding Catalyst illustrates a broader point: Students' outside lives and worldviews follow them on campus.

Haynes, the First Amendment scholar who has written guidelines on religion and public education, points out that there is nothing unconstitutional about students following the advice of a mentor outside school.

In fact, Mr. Waggoner and other observers of religion in education say they believe that student-led groups often begin at the instigation of a parent, youth pastor, imam, rabbi, or member of a number of evangelical Christian organizations that regard public schools as their mission field.

Many such evangelical groups have increasingly targeted students, spurred by a belief that most born-again Christians made their commitment to Christ before they turned 14. Some adopt an aggressive approach; others opt for a ministry of presence. Yet others are choosing "a third alternative," says Professor Grelle, "which is to hold onto a robust Christian identity while at the same time meaningfully engaging with religious diversity in a way that is not primarily for the purposes of religious conversion."

Shin Kasahara seems to embody this approach in his public high school in Rome, Ga. A senior with hair brushed so far forward it almost obscures his eyes, Shin has a steady girlfriend, works evenings and weekends at McDonald's, and loves jujitsu. He is also part of Friend2Friend (F2F), a Youth for Christ ministry he credits with helping him find "a better way to talk with friends about Christ in school."

F2F encapsulates its approach in a catchy slogan – Share-Pray-Discover – and in materials with passages that sound like instructions on "how to infiltrate schools." But what emerges from conversations with F2F leaders and with Shin himself is a stress on respect for and curiosity about others. It is a combination that allows him to be entirely himself in the schoolyard, he says.

And if his buddies don't want to hear about Jesus? "We still hang out," he says.

Interfaith dialogue in Mormon country

Classes had ended at Brighton High School in Cottonwood Heights, Utah, and students were streaming out the door when one stooped to pick up some papers off the floor. Immediately, she recognized that the text was torn from a book that she and 80 percent of the town's residents deem holy. More pages were scattered down the hall, strewn beside the outside walkway, skittering across the parking lot, plastered on the grilles of parked cars. Her tears welling up, she dashed back into the building to stand, arms clamped around torn and crumpled pages, in the doorway of Jodi Ide's classroom. She cried to her teacher: "Someone ripped up the Book of Mormon. I tried to get ... all [the pages]."

The next day, Ms. Ide, herself a member of the Church of Jesus Christ of Latter-day Saints, arranged the desks in a circle. She knew by then that the student responsible was in her class. She also knew that disciplinary action would not get at the root of the problem.

"Help me understand how this would happen," she asked her students. After a moment, one said, "It's not always easy growing up here if you're not Mormon." A couple of others chimed in: Some people won't invite you to their birthday parties, they say, and some guys won't even think about dating you. Even back in kindergarten, some kids say, "You're not Mormon? You're going to hell."

"That shouldn't happen," a Mormon girl said, visibly upset. "I am so, so sorry."

Then Ide watched as Mormons spoke about not knowing how to reach out to someone who thought Mormon beliefs were absurd; and non-Mormons related how they felt all Mormons wanted was to convert them. Confusion, fear, embarrassment, frustration, and hurt poured into the circle. Nobody condoned "the hateful act," but they understood its context; more important, they understood each other.

It was no accident that this unfolded in Ide's classroom; it's where Brighton students come to learn about world religions and, for the past two years, discuss worldviews and religious practice with peers as far away as the Philippines and Indonesia. They do this via video-conference as part of Face to Faith, a project of former British Prime Minister Tony Blair's Faith Foundation.

Programs like this bolster Mark Chancey's conviction that "religious literacy is essential." A professor of religious studies at Southern Methodist University in Dallas, Mr. Chancey says, "we all need to know about each other as our country becomes more diverse because we all have to get along."

The experience of Modesto, Calif., helping to keep peace through religion, underscores this. It's a heavily Hispanic community with large evangelical Christian, Sikh, Buddhist, and Muslim communities. Since 2000, the central California school district has been the only district in the United States to make a world religions class a graduation requirement, says Haynes.

"It supported the safe school policy," explains Jennie Sweeney, then the district's social science curriculum coordinator. "We knew that the more knowledge we could give the students, the better they would get along with each other."

Students sometimes poked fun at a boy for wearing "that handkerchief on his head" or got their noses out of joint when a girl made excuses to not eat lunch with friends. As the class progressed, it started to dawn on students: the boy was a Sikh; the girl was fasting for Ramadan.

Talking about the basics of different faiths made it easier for students to ask questions and volunteer information.

"When 9/11 occurred or, more recently, the Boston bombings," Ms. Sweeney says, "we didn't have any problems with hostilities toward our Muslim students."

Across the country in New York, ninth-graders at Townsend Harris High School also learn about religions as part of a mandatory Advanced Placement World History class.

"I don't challenge whether Moses received the Ten Commandments from God or whether Jesus performed miracles," says history teacher Franco Scardino. "I ask the students to think through why this message takes hold and resonates. Or why monotheism evolves on the Arabian Peninsula in a nomadic society where polytheism is all around them."

His approach conforms with the 1963 Supreme Court decision that specifically encouraged "teaching about religion, as distinguished from the teaching of religion."

The ruling also approved the "non-devotional use of the Bible in public schools," which, Chancey explains, means "you're teaching factual material about what religious traditions believe." He believes all Americans should know the Bible and its influence. But, he cautions, "it is one thing to say 'Jews and Christians believe the Bible is inspired by God'; it is an entirely different thing to teach 'the Bible is inspired by God.' "

Analyzing the 2011-12 curricula of Bible classes taught in 57 school districts in Texas, however, he found this nuance lost in all but 11. Commissioned by the Texas Freedom Network, Chancey's study also reports that when sectarian bias occurred, it favored views associated with conservative forms of Protestantism. The bias, he says, can creep in through flawed materials – he singles out publications of the North Carolina-based National Council on Bible Curriculum in Public Schools – or through teachers who simply lack the proper training.

Meanwhile, in Room 411 at Townsend Harris, Mr. Scardino projects a quote on a screen: "Give to Caesar what is Caesar's and to God what is God's. Mark 12:17."

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The week before, the 30 freshmen had teased out what tenets of Islam spurred Muslims in Baghdad to make scientific discoveries, create hospitals, and distribute books. In a future class they will discuss the role of faith in medieval Europe. But today, students of many faiths and no faith grapple with the relationship of church and state, unaware that they themselves are shaping that work in progress.

Correspondent Lee Lawrence spoke about this article and her reporting with C-SPAN on June 19.