Described herein is a method of calibrating a display in a head-mounted display system. The system includes a frame for maintaining the display in front of the user's eyes, and one or more lenses disposed between the display and the user's eyes. The method is configured to be performed by a computer processor associated with the head mounted display system and includes the steps of: a) generating a first image on the display based on predetermined parameters, the image including a two dimensional calibration structure identifiable by the user; b) receiving user input to generate a corrected image on the display; c) deriving calibration data based on the received user input and the predetermined parameters; and d) applying the calibration data to subsequent images generated on the display.