Poly-acrylic acid (PAAc) terminated silicon nanoparticles (SiNPs) have been synthesized and employed as a synchronous fluorescent signal indicator in a series of cultured mammalian cells: HHL5, HepG2 and 3T3-L1. Their biological effects on cell growth and proliferation in both human and mouse cell lines have been studied. There was no evidence of in vitro cytotoxity in the cells exposed to PAAc terminated SiNPS when assessed by cell morphology, cell proliferation and viability, and DNA damage assays. The uptake of the nanocrystals by both HepG2 and 3T3-L1 cells was investigated by confocal microscopy and flow cytometry, which showed a clear time-dependence at higher concentrations. Reconstructed 3-D confocal microscope images exhibited that the PAAc-SiNPs were evenly distributed throughout the cytosol rather than attached to outer membrane. This study provides fundamental evidence for the safe application and further modification of silicon nanoparticles, which could broaden their application as cell markers in living systems and in micelle encapsulated drug delivery systems.