(ABC News) -- Coy Mathis, born a male triplet, has behaved like a girl since she was 18 months old. When her brother Max was consumed with dinosaurs, she was playing with Barbie dolls. By 4, she was telling her mother that something was wrong with her body.
Since being enrolled at Eagle Elementary School in Fountain, Colo., the 6-year-old has presented as female and wearing girls' clothing. Her classmates and teachers have used female pronouns to refer to her, and she has used the girls' bathrooms.
But since December, school officials have told her parents she can no longer use the female facilities and ordered her to use the boys' or nurse's bathroom.
"We want Coy to have the same educational opportunities as every other Colorado student," said Kathryn Mathis, Coy's mother. "Her school should not be singling her out for mistreatment just because she is transgender."
Now Jeremy and Kathryn Mathis, with the help of the Transgender Legal and Defense Education Fund (TLDEF), have filed a complaint with the Colorado Civil Rights Division on behalf of Coy, alleging that the school has violated her rights. Since Christmas vacation, Coy has been homeschooled.
"Our eye is focused on getting Coy back into school," said TLDEF's executive director Michael Silverman. "We are hopeful we can resolve this quickly for Coy's sake."
Fountain school district's press spokesman John Fogarty did not immediately return calls seeking comment.
But a letter from the school's lawyers said, "The district's decision took into account not only Coy but other students in the building, their parents, and the future impact a boy with male genitals using a girls' bathroom would have as Coy grew older."
While other students and teachers do not notice that Coy has male genitals, the school said it feared as the child developed parents and students would become "uncomfortable."
"...It would be far more psychologically damaging and disruptive for the issue to arise at an age when students deal with social issues," the letter said.
Across the nation, schools are paying more attention to transgender issues, but there is little uniformity. Some Colorado schools, including Boulder Valley Schools, have detailed policies, according to a report on Coy's case in the Denver Post.
The Colorado Anti-Discrimination Act prohibits discrimination against transgender students in public schools.
A report by the National Center for Transgender Equality and the National Gay and Lesbian Task Force paints a bleak picture of life as a transgender person in the United States. The 2011 survey, "Injustice at Every Turn," found that discrimination is pervasive in "nearly every system and institution."
Transgender youth, in particular, are at disproportionate risk for depression, suicide, substance abuse, HIV and sexually transmitted diseases, according to the Family Acceptance Project at San Francisco State University.
Coy's parents worry that the school's policy is setting their child up for stigma and bullying.
"We have five children and we love them all very much," said Kathryn Mathis. "We want Coy to return to school to be with her teachers, her friends, and her siblings, but we are afraid to send her back until we know that the school is going to treat her fairly. She is still just 6 years old, and we do not want one of our daughter's earliest experiences to be our community telling her she's not good enough."
The Mathis' have a set of triplets and two other children, Dakota, 8, and Auri, 2. The father, Jeremy Mathis, 31, is a former Marine who was honorably discharged with injuries. Kathryn Mathis, 27, is a certified nurse assistant and takes care of Coy's triplet, Lily who has been severely disabled since a viral infection after birth. She must be fed through an IV and is quadriplegic.
"Coy's school has the opportunity to turn this around and teach Coy's classmates a valuable lesson about friendship, respect and basic fairness," said Silverman, who is representing the family in their complaint.
He said the family has known since Coy was a baby that she was struggling with gender identification.
When Coy began complaining about "something wrong" with her body, her parents took her to a specialist, who diagnosed gender identity disorder. Doctors recommended no immediate medical intervention but to let her "live as a girl," he explained. "They spoke to the school and they said, 'fine.'"
Since kindergarten, Coy has presented as female. Some of the school's bathrooms had no gender designation, but for those that did, she used the girls' facilities.
Silverman said that when the family was notified that the little girl would no longer be allowed to use the girls' bathroom, they were not aware of any complaints from parents or other students.
"It was a seemingly placid situation at the school," he said.
TLDEF wrote a letter to the elementary school hoping they would reconsider. "They said, 'no,'" according to Silverman.
The decision of the civil rights board is binding, so if an agreement can't be reached, either side can appeal to the courts.