An exposure apparatus includes a substrate stage movable while holding a substrate, a substrate alignment system which detects an alignment mark (1) on the substrate held by the substrate stage and detects a reference mark (PFM) provided on the substrate stage, and a mask alignment system which detects, via a projection optical system, a reference mark (MFM) provided on the substrate stage. The reference mark (PFM) on the substrate stage is detected without a liquid by using the substrate alignment system, and the reference mark (MFM) on the substrate stage is detected using the mask alignment system via the projection optical system and the liquid. Then, a positional relationship between a detection reference position of the substrate alignment system and a projection position of an image of a pattern is obtained, thereby accurately performing alignment processing in the liquid immersion exposure.