In a method of aligning a wafer stage, the wafer stage may be moved in an X-axis direction. A first coordinate of the wafer stage may be measured from a first measurement position inclined to the X-axis. The wafer stage may be moved in a Y-axis direction. A second coordinate of the wafer stage may be measured from a second measurement position inclined to the Y-axis. Thus, a movement distance of the wafer stage may be increased, so that the interferometers may accurately measure the position of the wafer stage.