Had that question a week ago when on a trip to Florida. I let it cool about 5 or 10 minutes then put the cover on. Had just ridden 2 to 3 hours without stopping and the bike was fully heated up. My concern was not the headers as they were cool enough but rather all the heat in the engine radiator etc. The bike was fine with no problems. My cover fastens under the headers so I have to wait till they are cool but as other have said they cool quickly - be careful about the touch test to see how cool they are. When I arrived at the beach I parked behind the building we were staying in but the bike was in the direct path of the wind coming off the beach! Since the wind was blowing about 30 MPH due to storms going thru there a lot of salt spray was in the air - bike cooled really quick though! I put the cover on after about 5 minutes but didn't get it totally pulled down over the rear sprocket which resulted in some rust on the chain and a discolored place on the sprocket, not a problem as I'm going to replace them very soon anyway.