According to example embodiments, a method of operating an exposure apparatus including a stage having a plurality of beam measurement devices, and an exposure head unit having a first set of exposure heads and a second set of exposure heads includes measuring a position of a first exposure head of the first set of exposure heads by moving the stage to coincide a first beam measurement device of the plurality of beam measurement devices with the first exposure head, setting the measured position of the first exposure head as a reference position, and measuring positions of the second set of exposure heads with respect to the reference position.