The NA60 experiment at the CERN SPS studies dimuon production in nucleus-nucleus and proton-nucleus collisions. The NA60 experimental program requires accurate tracking in the vertex region. In particular, it is crucial to distinguish between dimuons coming from the interaction vertex and muon pairs coming from the decay of charmed mesons. The high multiplicity of charged tracks produced in heavy-ion collisions imposes the use of radiation tolerant silicon pixel detectors. The NA60 silicon vertex detector is made of 16 planes, providing 11 tracking points. It was commissioned in the summer of 2003 and used in a 40-day-long data taking period in October/November 2003. This paper describes the detector, its performance and results from the 2003 Indium-Indium run.