Silicon quantum dots (QDs) have been proposed for use as luminescent biological probes. Along with the general advantages of quantum dots over traditional fluorescent dyes, such as brighter emission, photostability, and the ability to excite dots with multiple emission wavelengths using a single excitation source, interest in silicon quantum dots for biological applications is driven by their perceived low toxicity. Given the low toxicity of bulk silicon and porous silicon, this is a reasonable expectation. However, the biocompatibility of free silicon nanoparticles remains to be investigated. We have recently demonstrated in vitro fluorescence imaging using Si quantum dots in live cells. While we did not observe any acute toxicity in that study, no thorough investigation of cytotoxicity of silicon nanoparticles, or the dependence of cytotoxicity on the method of synthesis or surface modification, has been presented. Thus, in the work to be described here, we have measured the cytotoxic effect of luminescent silicon quantum dots. Bare (as prepared), organic ligand functionalized, micelle encapsulated, protein conjugated, and antibody conjugated silicon quantum dots were incubated with pancreatic cancer cells. Dose dependent cytotoxicity was evaluated using an MTS viability assay, for a wide range of Si QD concentrations. Our results confirm that silicon nanoparticles synthesized by laser pyrolysis are relatively non-toxic to cells. However, depending on the method of surface functionalization of the particles, some apoptosis may occur. In the range typically used for biological imaging, all of the silicon nanoparticle preparations were relatively non-toxic, confirming their potential for use as biocompatible imaging agents.