A new type of quantum dot (QD) ligand chemistry is introduced that can provide positive, negative, or zwitterionic surface QDs. CdSe/CdZnS core-shell QDs are decorated with ligands, and the non-specific and specific interactions of the QDs through their surface charge are investigated with the focus on cellular adsorptions and endocytosis. Zwitterionic QDs are compact with a ligand hydrodynamic thickness of less than 2 nm, they are colloidally very stable over a broad pH range and even in saturated NaCl solution, and they show minimal non-specifi c adsorptions. Positive and negative QDs show a very different behavior for cellular adsorption and subsequent incorporation, suggesting mostly energy-independent pathways for positive QDs and exclusively adenosine triphosphate (ATP)-dependent pathways for negative QDs. The zwitterionic QD surface ligands can also be used in conjunction with other functional groups, which allows simple conjugations for highly specific targeting whereas retaining the advantages of a zwitterionic QD surface. This QD surface chemistry can provide highly specifi c and very sensitive imaging with very low background level. Using the mixed QD surface ligand system, we demonstrated streptavidin and antibody QD conjugates that show a signal-to-noise ratio that is over 4000 times higher than the unconjugated mixture, which was used as a control case. The QD chemistry reported herein can be easily extended to other functional groups, such as alkynes, azides, or other amines, and can be further used in many future applications, including single-QD level experiments, sensitive assays, or in vivo applications using anti-fouling QD probes.