The mechanical behaviour of a rock mass is significantly controlled by the presence of discontinuities, and understanding the effect of discontinuities is essential in the economical and reliable design of rock structures. This research investigated the effect of roughness and persistency of rock joints on the mechanical behaviour of rock structures using the Particle Flow Code (PFC). In PFC, the intact material is represented by an assembly of particles bonded together. Traditionally, joints have been modelled in PFC using either the bond removal method or the smooth joint model. Analyses undertaken in this research showed that these approaches are not able to reproduce the shear behaviour of rock joints. To overcome this problem, a new shear box genesis approach was proposed. The ability of the proposed method in reproducing the shear behaviour and asperity degradation of rock joints was investigated by undertaking a comparative study against analytical and empirical models, as well as experimental direct shear tests on synthetic joints under different normal stresses whereby good agreement was found. To overcome existing problems in the determination of the shear behaviour of rock joints, a combination of photogrammetry and numerical modelling was proposed. Results indicated this approach has the ability to reproduce the shear behaviour of rock joints. The proposed method was employed to investigate the effect of scale on the shear behaviour of rock joints. It was found that the mobilisation of different order asperities for different joint lengths resulted in the negative scale effect on the peak shear strength. The effect of joint geometrical parameters of non-persistent joints on the mechanical behaviour of jointed rock masses was numerically investigated. A validation study was undertaken by uniaxial and biaxial compression tests, and the numerical analyses were found to correlate well with physical experimentation at low confining pressures. This was followed by a sensitivity study on the effect of joint configuration parameters on the failure mode, unconfined compressive strength, and deformation modulus. The insights presented in this study have improved understanding of the effect of joint roughness on the shear behaviour, and the process of damage evolution of rock joints as well as the effect of joint geometrical parameters on the mechanical behaviour and failure mechanism of non-persistent joints.