The development of molecularly targeted probes that exhibit high biostability, biocompatibility, and efficient clearance profiles is key to optimizing biodistribution and transport across biological barriers. Further, coupling probes designed to meet these criteria with high-sensitivity, quantitative imaging strategies is mandatory for ensuring early in vivo tumor detection and timely treatment response. These challenges have often only been examined individually, impeding the clinical translation of fluorescent probes. By simultaneously optimizing these design criteria, we created a new generation of near-infrared fluorescent core-shell silica-based nanoparticles (C dots) tuned to hydrodynamic diameters of 3.3 and 6.0 nm with improved photophysical characteristics over the parent dye. A neutral organic coating prevented adsorption of serum proteins and facilitated efficient urinary excretion. Detailed particle biodistribution studies were performed using more quantitative ex vivo fluorescence detection protocols and combined optical-PET imaging. The results suggest that this new generation of C dots constitutes a promising clinically translatable materials platform which may be adapted for tumor targeting and treatment.