A projection exposure apparatus is disclosed, including a focal plane measuring system (8) and an alignment measuring system (9) both disposed between a reticle stage (3) and a substrate stage (4). The alignment measuring system (9) is capable of focusing. The focal plane measuring system (8) measures variation in the surface profile of a substrate (5), and the alignment measuring system (9) effectuates focusing based on data obtained from the measurement performed by the focal plane measuring system (8). After the completion of the focusing, coordinates of various points on the substrate (5) in the alignment measuring system (9) are those of the points that have experienced the profile variation of the substrate (5). A relative positional relationship between the reticle (2) and the substrate (5) that has undergone the profile variation can be computationally derived from the changes in the coordinates of the points, and compensation can be accomplished by moving the substrate stage (4). In this way, even when there are differences between measuring focal planes of the alignment measuring system (9) and the focal plane measuring system (8), the resulting errors can be compensated for through calculation and focusing. An exposure method for a projection apparatus is also disclosed.