Posting on his official Twitter account earlier this week, the writer claimed that he finds watching the Fox sitcom to be uncomfortable.
He wrote: "I like the idea of Glee but why is it that every time I watch an episode I feel like I've stepped into a puddle of HIV?"
Responding to criticism of his comments from Twitter followers on Wednesday night, Ellis suggested that watching Glee star Chris Colfer sing on an episode shown this week prompted him to condemn the series.
"No, I wasn't drunk last night. I was watching Chris Colfer singing, um, "Le Jazz Hot" and felt like I had suddenly come down with the hivs (sic)," the novelist added.
Ellis made provocative remarks last summer, when he suggested his excessive drug use was fuelled by living in New York City.
Glee airs Tuesdays at 8pm ET/7pm CT on Fox.
> 'Glee' to include more original songs