A disk drive is disclosed comprising a disk having top and bottom surfaces, and top and bottom heads actuated over the top and bottom surfaces, respectively. Control circuitry detects a warping of the disk by writing a first test pattern to the top surface, reading the first test pattern to generate a first read signal, monitoring a first read signal value proportional to an amplitude of the first read signal, writing a second test pattern to the bottom surface, reading the second test pattern to generate a second read signal, monitoring a second read signal value proportional to an amplitude of the second read signal, and processing the first and second read signal values to detect a negative correlation between the amplitudes of the first and second read signals.