Cyclic shear test system, which is capable of measuring flow rate inside rock joint, was established to investigate the hydraulic behavior of rough rock joints under various loading conditions. Laboratory hydraulic tests during compression and shear were conducted for artificial rough rock joints. Prior to tests, aperture characteristics of specimens were examined by measuring surface topography. Permeability changes under compression were well approximated with several hydraulic model. Hydraulic behavior conformed to dilation characteristics in the first stage, and permeability increased with increase of dilation. As the shear displacement progressed, flow rate became somewhat constant due to gouge production and offset of apertures. Hydraulic behavior under cyclic shear loading was also influenced by the degradation of asperities and gouge production. In addition. the relation between hydraulic aperture and mechanical aperture under compression and shear loading was investigated and compared.