The Gay and Lesbian Alliance Against Defamation awarded "Grey's Anatomy" for the episode "Where the Boys Are."
The show got unwanted attention last year when actor Isaiah Washington used a slur to talk about a castmate in an on-set dustup. He later apologized and sought counseling.
"Little Miss Sunshine" won outstanding film in the wide release category, while "Ugly Betty" won for outstanding television comedy series and "Brothers & Sisters" took home the outstanding drama series award.
La Opinion newspaper was awarded outstanding Spanish-language newspaper for overall coverage.
The Vanguard Award went to actress Jennifer Aniston for her efforts to increase visibility and understanding of the lesbian, gay, bisexual and transgender community.
Tennis great Martina Navratilova was given the Stephen F. Kolzak Award, in honor of the late casting director who fought homophobia in the entertainment industry.
The 18th annual GLAAD Media Awards consisting of 42 categories are split into four ceremonies, held in Los Angeles, New York, Miami and San Francisco in March, April and May.
The awards "recognize and honor mainstream media for their fair, accurate and inclusive representations of the lesbian, gay, bisexual and transgender ... community and the issues that affect their lives."