Former AFL player Stephen Milne will face trial on rape charges over an alleged incident in 2004.

Magistrate Peter Reardon on Friday ruled there was sufficient evidence for Milne to stand trial on three of the four rape charges.

The 33-year-old has been charged with raping a woman in the Melbourne home of former St Kilda teammate Leigh Montagna.

The Melbourne Magistrates Court heard that the woman, who was 19 at the time, thought she was with Mr Montagna when the rape allegedly occurred in a darkened bedroom.