It could be wheels out of dish, a bent frame, a bent fork, or bent saddle rails, or some combination of these. Wheels are easiest to check - remove the wheel from the bike, flip it around and re-install - the wheel should be in exactly the same place WRT the frame or fork. The position of the wheel can also be indicative of frame or fork misalignment - if the wheel isn't easily centred between the seat stays and the chainstays, or between the fork legs, and you know the wheel to be true and properly dished, then there is something amiss with the frame or fork.