A method and system for calibration and compensation of color in a three dimensional display system includes user calibration of individual color channels using a multiplicity of grey screens while viewing with three dimensional glasses. Look-up tables are generated to ease conversion of input pixels to color corrected pixels to pre-distort the color of the pixels being driven by the three dimensional display system. Input pixels are then converted using the look-up tables and color corrected frames are displayed to a user. The pre-distortion effect allows a user to perceive colors in the three dimensional system as intended with the distortions caused by the viewing glasses and other aspects of the three dimensional display system.