Lithium-ion batteries (LIBs) containing silicon negative electrodes have been the subject of much recent investigation because of the extremely large gravimetric and volumetric capacity of silicon. The crystalline-to-amorphous phase transition that occurs on electrochemical Li insertion into crystalline Si, during the first discharge, hinders attempts to link structure in these systems with electrochemical performance. We apply a combination of static, in situ and magic angle sample spinning, ex Situ 7 Li nuclear magnetic resonance (NMR) studies to investigate the changes in local structure that occur in an actual working LIB. The first discharge occurs via the formation of isolated Si atoms and smaller Si-Si clusters embedded in a Li matrix; the latter are broken apart at the end of the discharge, forming isolated Si atoms. A spontaneous reaction of-the lithium silicide with the electrolyte is directly observed in the in situ NMR experiments; this mechanism results in self-discharge and potential capacity loss. The rate of this self-discharge process is much slower when CIVIC (carboxymethylcellulose) is used as the binder.