Tucked away in a document on reducing sexual assault at school – part of an unprecedented effort by the Obama administration to address such abuse – the Department of Education included a historic guideline extending federal civil rights protections to transgender students on Tuesday.

Title IX – the civil rights law that prohibits sex discrimination in federally funded education programs and activities – also bars discrimination on the basis of gender identity, announced the Department of Education’s Office for Civil Rights, marking a major victory in the fight to codify LGBT protections into federal law.

“Title IX’s sex discrimination prohibition extends to claims of discrimination based on gender identity or failure to conform to stereotypical notions of masculinity or femininity and OCR accepts such complaints for investigation,” reads the 46-page document. “Similarly, the actual or perceived sexual orientation or gender identity of the parties does not change a school’s obligations. Indeed, lesbian, gay, bisexual, and transgender (LGBT) youth report high rates of sexual harassment and sexual violence. A school should investigate and resolve allegations of sexual violence regarding LGBT students using the same procedures and standards that it uses in all complaints involving sexual violence.”

Though aimed at clarifying how Title IX relates to sexual violence, the guidance carries far broader implications. LGBT advocates note that transgender students will not just be explicitly protected from physical or sexual abuse under Title IX, but from all forms of discrimination in education.

“It certainly would be our view that transgender students should be given the ability to participate in sex segregated activities, like sports teams, consistent with their gender identity,” said Ian Thompson, legislative representative at the American Civil Liberties Union, to msnbc. “Failure on part of the school to allow that would be discrimination against that student.”

The Department of Education’s guidance builds off numerous court decisions and a 2012 opinion by the Equal Employment Opportunity Commission (EEOC) that gender identity discrimination falls under sex discrimination, which is barred by Title VII of the 1964 Civil Rights Act. Two other areas of federal law that explicitly protect individuals on the basis of gender identity and sexual orientation include hate crime legislation (the Matthew Shepard and James Byrd, Jr. Hate Crimes Prevention Act) and domestic violence legislation (the Violence Against Women ACT.)

However, in other areas areas of daily life – including housing and employment, for example – LGBT individuals remain vulnerable.

“There’s clearly a tremendous amount of work still to be done,” said Thompson. “The important point is in the absence of explicit protections in federal statutes.”

While the Department of Education’s document on sexual violence is a good start, the ACLU would now like to see OCR follow up with a comprehensive explanation on how Title IX protects transgender students from discrimination, and what steps schools should take to be in line with that law. Additionally, said Thompson, Congress should pass the Student Non-Discrimination Act to fully guarantee explicit nondiscrimination protections based on sexual orientation and gender identity in public K-12 schools.

“This guidance is very helpful, and having OCR take this position with respect to Title IX is very significant,” said Thompson. “But it should not be read as a substitution for explicit sexual orientation and gender identity nondiscrimination protections being put into place with a federal statute.”