Si is an important anode material for the next generation of Li ion batteries. Here the energetics and dynamics of Li atoms in bulk Si have been studied at different Li concentrations on the basis of first principles calculations. It is found that Li prefers to occupy an interstitial site as a shallow donor rather than a substitutional site. The most stable position is the tetrahedral (Td) site. The diffusion of a Li atom in the Si lattice is through a Td-Hex-Td trajectory, where the Hex site is the hexagonal transition site with an energy barrier of 0.58 eV. We have also systematically studied the local structural transition of a LixSi alloy with x varying from 0 to 0.25. At low doping concentration (x = 0-0.125), Li atoms prefer to be separated from each other, resulting in a homogeneous doping distribution. Starting from x = 0.125, Li atoms tend to form clusters induced by a lattice distortion with frequent breaking and reforming of Si-Si bonds. When x ≥ 0.1875, Li atoms will break some Si-Si bonds permanently, which results in dangling bonds. These dangling bonds create negatively charged zones, which is the main driving force for Li atom clustering at high doping concentration. © 2010 IOP Publishing Ltd.