Recent developments in nanotechnology have made available a host of new approaches for the improved quantitative detection of biomarkers due to the enhanced sensitivity of nanoparticle-based assays. The majority of molecular toxicology studies revolve around sensitive measurement of cell-death (apoptosis) and cell-health biomarkers present in living cells or formalin-fixed and paraffin embedded (FFPE) tissue samples. In this regard, semi-conductor quantum dots (QDs) which exhibit high brightness, photo-stability and degree of multiplexing, are predicted to have a significant impact on research in molecular toxicology. Due to these superior photophysical properties of QDs as compared to traditional fluorophores and the unsurpassed versatility of QDs as enabling components for new assays, these nanoparticles promise to facilitate new discoveries in molecular toxicology. Indeed, multiplexed QD-based assays have been incorporated into cell imaging, flow cytometry and other homogenized sample-based assays for detecting multiple biomarkers including those associated with cell injury and apoptosis.