Im honestly not sure. I know this ECU came out of another GLI. The only way I would think that the transmission would make a difference is if it was an automatic. I say that because the computer would control the transmission as well. With a manual, the computer doesnt control anything obviously, so I don't see any reason why it wouldn't work with a 5spd tranny as well as a 6spd as long as we are talking manual.
