Herein, we report on the functionalization of silica nanoparticles with a small molecule, the amino add cysteine, in order to create a low-fouling zwitterionic surface for nanomedicine applications. The cysteine functionalization was shown to impart the particles with excellent stability in both salt and single-protein solutions of lysozyme (positively charged) and bovine serum albumin (negatively charged). Bare silica particles precipitated immediately in a lysozyme solution, while cysteine-functionalized particles were stable for 20 h. Furthermore, the particles displayed excellent long-term stability in solutions of human serum showing no aggregation over a period of 14 days. The functionalized particles also possess multiple reactive surface groups for further coupling reactions. We believe that the surface functionalization schemes described in this report represent a versatile and effective method of stabilizing nanoparticle systems in biological media for their use in a variety of therapeutic and diagnostic applications.