For the mechanical stability assessment of a deep underground high-level waste repository. computer simulations using FLAC3D were carried out and important parameters including stress ratio, depth, tunnel size, joint spacing, and joint properties were chosen from sensitivity analysis. The main effect as well as the interaction effect between the important parameters could be investigated effectively using fractional factorial design . In order to analyze the stability of the disposal tunnel and deposition hole in a discontinuous rock mass, different modelings were performed under different conditions using 3DEC and the influence of joint distribution and properties, rock properties and stress ratio could be determined. From the three dimensional modelings, it was concluded that the conceptual repository design was mechanically stable even in a discontinuous rock mass.