An exposure apparatus for exposing shot areas on a substrate comprises a measuring device configured to measure a position of an alignment mark in each of the shot areas on the substrate, and a controller configured to generate sample shot sets from the shot areas on the substrate, to cause the measuring device to measure the position of the alignment mark in each of the sample shot sets under each of measurement conditions, to calculate a shot arrangement based on the measured positions with respect to each of combinations of the measurement conditions and the sample shot sets, to calculate a variation of the shot arrangements calculated with respect to the sample shot sets with respect to each of the measurement conditions, and to display the variation calculated with respect to each of the measurement conditions.