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Provo's Brigham Young University and its Idaho counterpart were among 102 schools included on the "Shame List" on Monday by the advocacy group Campus Pride.
The list targets schools for their treatment of lesbian, gay, bisexual and transgender students, and labels campuses as the "absolute worst" for LGBT youths.
Shane Windmeyer, executive director of the North Carolina-based Campus Pride, said "Shame List" schools were selected based on two criteria. The campuses either requested exemptions to Title IX a federal education law that bans sex-based discrimination or have a history of discriminatory policies and rhetoric against LGBT students.
"If your values and religious belief system include bigotry or discrimination toward any group of people, put it on your admission brochure," Windmeyer said. "Otherwise, Campus Pride will do it for you."
Both BYU and BYU-Idaho are private schools, owned and operated by The Church of Jesus Christ of Latter-day Saints. And many other "Shame List" campuses represent religious schools, such as Arlington Baptist College, California Baptist University and Liberty University.
Earlier this year, BYU-Idaho applied for and received a Title IX exemption from the U.S. Department of Education, freeing the school from provisions of the sex discrimination law and ending a department investigation into the school, which had stemmed from a complaint by a transgender student.
In its application, BYU-Idaho President Clark Gilbert argued that transitioning to a different gender conflicts with teachings of the Utah-based LDS Church.
BYU-Idaho did not respond to a request for comment.
Windmeyer said BYU in Provo is one of the "Shame List" campuses that has a track record of LGBT discrimination.
Campus Pride was one of several organization that earlier this month sent a letter to Big 12 administrators calling for BYU to be excluded from consideration for membership in the athletic conference.
The school's entry on the "Shame List" also references recent reports of LGBT students being investigated for violating the BYU Honor Code which prohibits premarital sex, alcohol and other activities after they've reported sexual assault.
Windmeyer said BYU and BYU-Idaho are examples of how religious prejudice becomes entrenched in higher education.
"Sadly, students don't necessarily have a choice of whether or not they want to go to BYU," Windmeyer said. "It's oftentimes based on their faith and their family."
The LDS Church deferred comment to BYU.
In a prepared statement, BYU spokeswoman Carri Jenkins said that one of the foundational principles of the Honor Code is to treat others with respect.
"We have made clear that one's sexual orientation is not an issue at BYU," she said. "Anyone who is part of our community or visits our campus should be treated with respect and dignity."