Non-Equilibrium Green Function simulations of the effect of discrete ionised dopants and surface roughness in Silicon nanowire transistors show the strong presence of resonances in the transmission coefficients. These resonances or quasi-bound states are the main component in the screening of dopants and play an important role in the current flow. Resonances appear through a self-consistent calculation of the electron density and potential. In this work we study several examples that exhibit different types of resonances. We start with a single impurity case and gradually evolved to a complex case with several random impurities. Interface roughness in a very narrow nanowire could induce resonant cavities as is proven in this paper. The effect of these resonances in the current-voltage characteristic of the transistors is considered in detail.