Nanoparticle- and quantum-dot (QD)-based bioprobes are emerging as alternatives to small-molecule probes for in vitro and in vivo applications. However, their cellular interaction and cell uptake mechanism are significantly different from those of small-molecule probes and are extremely sensitive to surface ligands. These present a barrier in the development of nanoparticles and QDs as cellular probes. This work focused on the synthesis of various functionalized QDs with tunable surface charge, hydrophobicity, and functionalization with poly(ethylene glycol) (PEGylation) and their cellular interaction. We found that the surface functional groups of nanometer-sized probes significantly dictated their cellular interaction, subcellular localization, and cytotoxicity. A dose-dependent interaction was observed for all types of QDs, but the cationic surface charge or hydrophobicity would increase the cellular interaction as compared to the anionic surface charge. Cationic QDs rapidly entered cells and induced cytotoxicity, but hydrophobic QDs were stuck to the cell membrane and did not enter the cells. PEGylation of cationic QDs reduced their nonspecific binding and cytotoxicity, and a higher concentration of QDs was required for cellular entry. On the basis of these results, we were able to design different functionalized QD nanoprobes with balanced hydrophobicity and surface charge for cell membrane labeling and subcellular targeting. Mechanistic studies indicated a clathrin-mediated interaction and uptake for all types of QDs. The cellular interaction and uptake of 20-50 nm particles were primarily determined by their surface charges and ability to penetrate the cellular membrane, and the final destinations of the nanoparticles in the cell could be controlled by the appropriate design of surface ligands.