An exposure apparatus for exposing a substrate with an energy beam via a projection optical system and liquid (Lq), the apparatus comprising: a first stage that is capable of moving relative to the projection optical system; a second stage that is capable of moving independently from the first stage and of mounting the substrate; a detection system (RAa, RAb) for detecting a mark of a mask and a reference mark of the second stage via the projection optical system and via the liquid, the mask having a pattern that is to be formed on the substrate, a liquid immersion system for supplying the liquid to form an immersion area just below the projection optical system; and a drive system for moving each of the first and second stages such that each of the first and second stages is arranged opposite to the projection optical system and is moved away from below the projection optical system; a controller configured to control the drive system to move the first and second stages, one of which is arranged opposite to the projection optical system, relative to each other such that the other of the first and second stages comes close to or into contact with the one of the first and second stages, and to move the close or contacting first and second stages relative to the immersion area below the projection optical system so as to transit from one to the other of first and second states while the immersion area is maintained just below the projection optical system, the first state being a state in which the immersion area is maintained between the projection optical system and the first stage, the second state being a state in which the immersion area is maintained between the projection optical system and the second stage, wherein the controller is configured such that, after the transition from the first state to the second state and prior to start of the exposure for the substrate, the detection system detects the mark of the mask and the reference mark via the liquid, and wherein the controller is configured to control the drive system such that, in the exposure, the substrate is moved relative to the immersion area by the second stage. a first stage that is capable of moving relative to the projection optical system; a second stage that is capable of moving independently from the first stage and of mounting the substrate; a detection system (RAa, RAb) for detecting a mark of a mask and a reference mark of the second stage via the projection optical system and via the liquid, the mask having a pattern that is to be formed on the substrate, a liquid immersion system for supplying the liquid to form an immersion area just below the projection optical system; and a drive system for moving each of the first and second stages such that each of the first and second stages is arranged opposite to the projection optical system and is moved away from below the projection optical system; a controller configured to control the drive system to move the first and second stages, one of which is arranged opposite to the projection optical system, relative to each other such that the other of the first and second stages comes close to or into contact with the one of the first and second stages, and to move the close or contacting first and second stages relative to the immersion area below the projection optical system so as to transit from one to the other of first and second states while the immersion area is maintained just below the projection optical system, the first state being a state in which the immersion area is maintained between the projection optical system and the first stage, the second state being a state in which the immersion area is maintained between the projection optical system and the second stage, wherein the controller is configured such that, after the transition from the first state to the second state and prior to start of the exposure for the substrate, the detection system detects the mark of the mask and the reference mark via the liquid, and wherein the controller is configured to control the drive system such that, in the exposure, the substrate is moved relative to the immersion area by the second stage.