A method of driving shutter glasses of a display system includes generating a display panel driving signal which drives a display panel of the display system, where the display panel displays a left image and a right image, generating a second three-dimensional (“3D”) synchronizing signal based on a first 3D synchronizing signal and the display panel driving signal, generating a third 3D synchronizing signal by adjusting an intensity of the second 3D synchronizing signal, generating a shutter control signal, which controls a left shutter and a right shutter of the shutter glasses, based on the third 3D synchronizing signal, and outputting the shutter control signal to the shutter glasses.