NEWBERG, Ore. — A growing number of openly transgender students have forced schools around the country to address questions so basic that they were rarely asked just a few years ago, much less answered: What defines a person’s gender, and who gets to decide?

A small Quaker college here, George Fox University, has become the latest front in this fight, refusing to recognize as male a student who was born anatomically female. The student calls himself a man, and as of April 11, when a state circuit court legally changed his sex, the state of Oregon agrees.

But George Fox University sees him as a woman, and it prohibits unwed students from living with anyone of the opposite sex. So when the student asked to live next year with a group of male friends, the university turned him down. Instead, it offered him a single-person apartment on campus, or off-campus housing.

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The dispute has drawn attention from two departments of the federal government. It has already broken new legal ground, and it might do so again soon, according to experts on gender identity issues.

At the center of it is Jaycen, a 20-year-old psychology major, who asked that his last name be withheld because he has been harassed and threatened. He is, in some ways, a typical young man — he is an avid basketball player, he is attracted to women and he spends spare hours playing the video game “Call of Duty” and listening to R&B and hip-hop.

“Living in a female dorm means that each day, the first thoughts I have are about my struggles living in a body that never felt right to me,” he said. Living there while undergoing testosterone therapy has been a particular challenge.

“I’ve got the libido of a 14-year-old boy, and I’m living with a bunch of young women,” he said. “It’s not a good recipe for promoting the kind of behavior that a Christian university expects from its students.”

In a California case that was settled last year, the federal government clearly adopted the position that under Title IX, the federal law barring sex-based discrimination in education, a school must accept a student’s gender self-identification, regardless of anatomy. Months later, Maine’s highest court ruled that state law required much the same thing, but other courts have disagreed. A federal appeals court ruled in 2009 that a school could bar a transgender woman from using the women’s restroom, because the school’s intent was not to discriminate, but to protect the safety and privacy of other women.

George Fox, which lies southwest of Portland, Oregon, asked the Department of Education for a religious exemption from Title IX. Rob Felton, a university spokesman, said the request was prompted by the position the government took in the California case, and by warnings from Jaycen’s lawyer that he intended to file a Title IX complaint. In drafting its petition, the university consulted with an evangelical group, Alliance Defending Freedom, that has fought attempts to allow transgender students to use what they see as the sex-appropriate school restrooms and other facilities.

The department granted the Title IX exemption on May 23, and on the same day it gave a similar exemption to Simpson University, a Christian school in California — the first two ever given for policies on transgender people, department officials and transgender advocates said. It granted a third exemption last month to Spring Arbor University, a Christian college in Michigan.

Now, the Justice Department is looking into whether George Fox’s transgender policy might violate nondiscrimination requirements in federal housing law. Advocates say that, too, would be a first.

George Fox administrators say that they have no animus toward transgender people, and that they have been respectful of Jaycen, including referring to him with male pronouns.

“I think the fact that Jayce is choosing to stay at George Fox shows the university community has been supportive of him during his whole experience here,” Felton said. “We may have a difference of opinion on appropriate housing, but all indications are he has been treated well by his peers, professors and our student life staff.”

Only a handful of disputes involving schools’ treatment of transgender students have come to light, and even fewer have resulted in formal complaints or lawsuits. In 2011, California Baptist University expelled a student for being transgender, an action that a state court upheld this month.

Some women’s colleges have said that a student who enrolled as female, and then began to transition to male, could remain enrolled. But one of those, Smith College in Massachusetts, made news last year by refusing to consider the application of a woman who was born anatomically male.

“What we’ve learned in the few cases that have gone forward is that the only humane and consistent way to determine a person’s sex is based on their lived experience as male or female, that any other approach, whether anatomy or chromosomes, will discriminate against some people,” said Jennifer Levi, director of the Transgender Rights Project at Gay and Lesbian Advocates and Defenders.

No college mentioned transgender people in its nondiscrimination policy until the 1990s, and most still do not. A small number have decided not to segregate housing or restrooms by sex, eliminating much of the need to determine who is female or male. Usually, it is not a matter of the colleges’ having policies that explicitly discriminate, but that “they haven’t really thought about it, they don’t have a stated policy and they would make decisions on a case-by-case basis,” said Genny Beemyn, director of the Stonewall Center at the University of Massachusetts at Amherst, who also tracks transgender policies at colleges around the country for Campus Pride, a national gay rights group.

Jaycen plans to have sex-reassignment surgery, but cannot afford it yet. The university says it will regard Jaycen as male if he undergoes surgery. “For 123 years, our housing policy has been to house students by their anatomy,” Felton said, adding that is “a question that a lot of institutions, religious and nonreligious, are struggling with.”

But many transgender people choose not to have those operations, or have only “top” or “bottom” surgery. But they often find that the world at large remains fixated on what anatomical features they have subtracted or added, not on how they identify themselves.

Colleges often go by whatever sex is indicated on an official document like a driver’s license or birth certificate, but policies on changing those documents vary widely from state to state.

Jaycen, who grew up in Portland and describes himself as deeply committed to his faith, began his transition to male more than a year ago; he quit the women’s basketball team when he started testosterone therapy. He seems outgoing and confident, but he says he suffers from depression, a common problem among transgender people, worsened by the strain of dealing with the university.

A study conducted by researchers at the American Foundation for Suicide Prevention and the Williams Institute at the University of California, Los Angeles, School of Law, released this year, concluded that people who identify as transgender or gender nonconforming attempt suicide at a rate that is nine times the national average.

Jaycen and his lawyer, Paul Southwick, negotiated for months with George Fox, trying to reach an informal agreement of some kind, though Southwick questioned whether the university was talking in good faith. He said that the university sought, among other conditions, to compel Jaycen to reveal his transgender status to his roommates, until he noted that that would violate federal law on student privacy. The roommates, in any case, already know, Jaycen said.

Southwick, a 2005 graduate of George Fox, has his own tangled history with the university. He said that when he was a student, despite a university policy banning pornography, a university counselor suggested that he might “cure” himself of being gay by watching heterosexual pornography.

Jaycen said that in spite of everything, he had found strong support from students and faculty members.

“I want other transgender and LGBTQ people to see that they can have a place in faith-based education,” he said. “The fact that I’m here is proof of that.”