A method to produce biocompatible polymer-coated silicon nanocrystals for medical imaging is shown. Silica-embedded Si nanocrystals are formed by HSQ thermolysis. The nanocrystals are then liberated from the oxide and terminated with Si-H bonds by HF etching, followed by alkyl monolayer passivation by thermal hydrosilylation. The Si nanocrystals have an average diameter of 2.1 nm ± 0.6 nm and photoluminesce with a peak emission wavelength of 650 nm, which lies within the transmission window of 650-900 nm that is useful for biological imaging. The hydrophobic Si nanocrystals are then coated with an amphiphilic polymer for dispersion in aqueous media with the pH ranging between 7 and 10 and an ionic strength between 30 mM and 2 M, while maintaining a bright and stable photoluminescence and a hydrodynamic radius of only 20 nm. Fluorescence imaging of polymer-coated Si nanocrystals in biological tissue is demonstrated, showing the potential for in vivo imaging.