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Religious exemptions from Title IX
If an educational institution is able to prove to the Department of Education that any provision of Title IX conflicts with a certain religious tenet of the organization, the Department grants an exemption. The educational institution is thus able to continue gender-based discrimination while receiving federal funding — as long as the institution's actions violate any other legislation. For LGBTQ+ students, Title IX is the only legislation that has been interpreted to protect them from discrimination in their educational institution, so a religiously exemption from Title IX leaves them undefended.

The religious exemption was based off the precedent of Representative Graham Purcell of Texas's amendment to JFK's 1964 Civil Rights Act, which allows religious educational institutions to discriminate in their hiring practices.

As of March 2019, 277 educational institutions are religiously exempt from Title IX.

Cases of discrimination against LGBTQ+ students
In 2012, the private Christian Grace University expelled Danielle Powell for her lesbian relationship. Grace University, which had a religious exemption from Title IX, argued Powell brought the expulsion on herself, as she signed an agreement to obey all the university's community standards her first year. This justification solidly placed the responsibility upon all LGBTQ+ students to choose their educational institutions with full knowledge of their community standards and religious exemption status. Additionally, Grace University assumed all LGBTQ+ students would have already self-identified as queer, when Powell herself had not yet recognized her LGBTQ+ identity when signing the community standards.

In 2014, a trans male student at George Fox University requested to live in campus all-male housing. The private Quaker college first refused his request, and then applied for a religious exemption from Title IX through the Office of Civil Rights. Even though the discrimination technically violated Title IX since the university had not obtained the exemption at the time of refusing the student's request, the Office of Civil Rights still granted the exemption and treated the discrimination as allowed, citing a "presumed" exemption based on those of similar institutions.

In 2018, Christian Pennsylvania school Clark Summit University expelled Gary Campbell for violating their "sexual purity" policy. He was six credits away from graduation after taking personal leave, and Clark Summit University had not applied for religious exemption from Title IX.