The pair were talking about an article reporting that a third of the population in Britain were unaware where Britain's largest cities -- London, Birmingham and Glasgow -- were on a map.
Wilkes, a friend of Robbie Williams, said: "Forget Glasgow, I thought Manchester was one of the three."
Homes replied: "What are you, a retard? Don't be stupid."
In a further gaffe, just seconds later, he looked red-faced as his mobile phone went off before the show cut to ads.
During the break, some viewers called in to complain. A number went on the show's Facebook page, calling for him to be sacked.
When the programme came back on air minutes later, Holmes apologised. He said. "I have to say sorry to three or four of you who are upset because I used the word retarded. You seem to have taken it personally or think I am being insulting. I would never want to do that. There is this man who has an autistic child and said I insulted his child. I would never use it in that context. Sorry if that caused you offence.'
He later reiterated his apology on his Twitter page and thanked his followers for their support.