A method and apparatus for controlling picture quality of a flat panel display capable of electrically compensating for a display defect of a display panel are disclosed. The method of compensating for a display defect of a flat panel display includes reading identification information of a display panel; generating positional information indicating the position of the display defect and the form of the display defect of the display panel on the basis of first input information and the identification information; generating a compensation value for compensating the degree of the display defect of on the basis of second input information; storing the positional information and the compensation value in a memory; and reading the positional information and the compensation value from the memory, modulating data to be displayed at the position of the display defect of the display panel by the compensation value, and displaying the modulated data on the display panel.