The precision cyclic shear test system was established to investigate the mechanical characteristics of rough rock joints under cyclic loading conditions. Laboratory cyclic shear tests were conducted for saw-cut joints and artificial rough rock joints using Hwangdeung granite and Yeosan marble. Surface roughness and aperture characteristics of specimens were examined by measuring surface topography using the laser profilometer. Peak shear strength, phase difference during loading and unloading, and anisotropic shear behavior were investigated throughout the cyclic shear test results. These features and their subsequent variations in each loading cycle are significantly dependent upon the second order asperities and the strength of intact rock. It was observed that degradation of asperities for rough rock joints under cyclic shear loading followed the exponential degradation laws of asperity angle and that the mechanism for asperity degradation would be different depending upon the normal stress level, roughness of joint surface and the loading stage.