I was also wondering about the reverse. I'll be flying on Air Canada to Vancouver from within Canada, and then on Japan Airlines to Tokyo, Japan, and then to my final destination, Nagoya, Japan. Are there any issues with me checking in online with Air Canada for the first leg of my itinerary if I will transfer to another airline? When I get to my departure airport, will I have to show the Air Canada check-in agent my printed online boarding pass and complete itinerary so that she will know that my final destination isn't Vancouver and therefore can tag my bags through to Japan even though I will be switching to Japan Airlines in Vancouver? I will be checking in online with Japan Airlines as well so I don't have to leave the post-security secure area when I arrive in Vancouver and just want to make sure that there won't be any issues with my bags or anything when I change planes and airlines. I've never done this before, so I'm a bit unsure.