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The actor, who plays homosexual Scotty Wandell in the US drama, decided to come out after shooting scenes in which his character marries lover Kevin Walker.
He told Canada's Globe and Mail: "I don't know what will happen professionally... that is the fear, but I guess I can't really be concerned about what will happen, because it's my truth.
"There is this desire in LA to wonder who you are and what's been blaring for me for the last three years is how can I be most authentic to myself - so this is the first time I am speaking about it in this way."
McFarlane added that he has made no secret of his sexuality around family and friends, but drew the line at revealing whether he is in a relationship.
The news has fuelled speculation that Prison Break star Wentworth Miller is also gay as the pair have been seen together on numerous occasions.
> Miller: 'I can't kill gay rumour'
