Atlanta, Georgia (CNN) -- When Kevin Murphy entered as a freshman at Mount Holyoke, a Massachusetts women's college, in 2003, he was female. By the time he received his diploma, he was male.

Phillip Hudson, who attended Morehouse, an all-male historically black college in Georgia, calls himself androgynous, meaning he doesn't identify with masculine or feminine identity norms.

The two men represent a debate that is brewing at some of the nation's same-sex colleges. For these colleges, which have historically defied boundaries and challenged the status quo, a new test of tolerance has surfaced: How are they handling gender identity?

Defining gender on same-sex campuses has become murky as some students say they fall outside the conventional male-female gender binary. More schools are encountering complicated cases where not all students at men's colleges identify as male and not all students at women's colleges identify as female.

The diversity of gender expression comes in many forms, from individuals who consider themselves androgynous or nongender-conforming to students who are transgender or in the process of changing their sex. Transgender people are often defined as those who do not identify with the gender they were at birth.

At Smith College, a women's institution in Massachusetts, the junior class president is Roth, who recently transitioned from female to male. Roth asked to be identified only by his first name.

At Morehouse College, the issue of cross-dressing students emerged on campus last year. A handful of the male students wore women's clothing, purses and high heels.

"You don't have to conform to one idea on what it means to be a masculine male in order to be successful, and the same way with women," said Shane Windmeyer, director of Campus Pride, a resource network dedicated to gay, lesbian, bisexual and transgender college students.

At the center of the controversy is whether men's and women's colleges should allow transgender or nongender-conforming students to stay on campus when the purpose of same-sex schools is to cater to a single gender. Same-sex schools continue to admit only a single sex, but once the student is enrolled, the rules are less clear.

Most schools don't have specific policies to address nongender-conforming or transgender students, said Genny Beemyn, who has studied transgender issues on campus and is on the board of the Transgender Law and Policy Institute, a nonprofit organization dedicated to transgender people. Only a little more than 300 out of 4,000 colleges have added gender status to their nondiscrimination protection clauses.

"Colleges don't think they have a need to do it, and in my opinion, that's a wrong mindset," Beemyn said. "It's reactionary, and it's waiting until you have a crisis before you do anything."

In 2003, a student-led initiative at Smith College replaced gender-specific language in the student government constitution such as "she" and "her" with more neutral terms. Other students have advocated for gender inclusiveness through the National Student Genderblind Campaign, a grassroots network that promotes gender-neutral policies.

Patricia VandenBerg, communications director at Mount Holyoke College, said the school does not have a specific policy to address transgender students or nongender-conforming students -- the only hard rule is that Mount Holyoke can admit only women.

"We admit women," VandenBerg said. "We graduate students. They develop as they develop."

On Morehouse's quaint campus, signs banning women's clothing are visible inside buildings. The rules have been strictly enforced, students say.

Last year, administrators implemented a dress code that no longer allowed women's apparel, including dresses, tops, purses and pumps. The administration declined to comment on the dress code, and the rules still stand, said Elise Durham, media relations manager at Morehouse.

Read about Morehouse's clothing ban passed last year

Kevin Webb, a Morehouse senior and president of the gay student group Safe Space, said parts of the dress code contradict the school's historic tradition of acceptance. He said the school should embrace a wide spectrum of male students, instead of imposing a narrow definition of masculinity.

"We are all humans, students," he said. "We should be able to experience things, including cross-dressing. If we take those moments away, we have failed them during the four years. We haven't allowed them to grow."

Identifying with a different gender can be challenging on college campuses, according to The 2010 "State of Higher Education for LGBT People" report by Campus Pride. The survey examined responses from more than 5,000 students, faculty members and administrators at colleges and universities across the U.S. and found that respondents who identified as transmasculine, transfeminine and nongender-conforming experienced higher rates of harassment.

Nearly 40 percent of transfeminine and transmasculine respondents experienced harassment on campus, the study showed. About 31 percent of nongender-conforming students experienced harassment.

In comparison, the study found that about 20 percent of men and women experienced harassment.

Phillip Hudson, 21, who identifies as androgynous, was a student at Morehouse studying communications last year when the women's clothing ban took place. Towering at more than 6-foot-4, he liked wearing makeup and lip gloss. He often sported his Marc Jacobs tote bag and Ugg boots on campus.

His fashion choices and sexuality sometimes brought harassment and ridicule on campus, he said.

"I do understand it's an all-male school," said Hudson, who transferred to a college in Florida this year. "If you want to have a uniform for us to wear, that's fine, but don't pass policies that are specifically targeting a few people."

Kevin Murphy, now 25, who entered Mount Holyoke as a woman and graduated as a man, said the school was safe and supportive. However, there were many times when he still felt left out.

"I often felt very lonely and lost a lot of people I cared about," he wrote in an e-mail.

Cade, a 19-year-old student from California at Mount Holyoke studying computer science, identifies as gender queer and is transitioning to become a male. Cade is planning on taking hormones this year.

"It's a very small percentage of the population that has that reaction," said Cade, who declined to give a last name for privacy reasons. "A lot times, it's, 'This is a women's space. Why are you here?' "

While little has been studied about nongender-conforming students on same-sex campuses, some academics are beginning to examine the issue. The topic also became a part of a Sundance documentary show called "TransGeneration" in 2005.

Colleges may view allowing the opposite gender -- or what is perceived to be the opposite gender -- to remain on campus to be damaging to the school's reputation, explains Susan Marine, assistant dean of student life at Harvard College in Massachusetts, who wrote a dissertation on women's colleges and transgender students.

After interviewing more than 30 administrators at women's colleges, Marine said there are concerns that alumni will react negatively to the idea of allowing cross-dressing or nongender-conforming students on campus. As a result, they could refuse to donate money to the school.

"The colleges are in a very unique position," she said. "How do they preserve their identity when student identities are being called into question?"

Some students say their same-sex colleges are welcoming when it comes to changing genders.

At Smith College, Roth, 20, said he was admitted to the school as a woman. He says he grew up in a conservative Asian-American household and was surprised to encounter a "whatever floats your boat mentality" from fellow Smith classmates.

During the second semester of his freshman year in 2009, he started taking hormones. He underwent top surgery last summer, a process that included the removal of his breasts.

"It [Smith] definitely helped me transition faster," said Roth, who, even as a man, was elected junior class president last year.