Baldwin's messages were directed at a newspaper reporter who accused his wife of tweeting during the funeral for the former star of "The Sopranos" James Gandolfini.
In the profanity-laden tweets, which have since been deleted, Baldwin called the reporter a "toxic little queen."
Baldwin says in a letter to GLAAD posted on its website Friday his tweets didn't have anything to do with "issues of anyone's sexual orientation."
The former "30 Rock" star says he's done political work with marriage equality groups and insists he wouldn't advocate violence against someone for being gay.
GLAAD spokesman Rich Ferraro says Baldwin's language was improper and his tweets didn't reflect his "history of actively supporting LGBT equality."