In this report, we evaluated the cytotoxicity of a series of quantum dots (QDs) directly synthesized in aqueous phase, i.e., thiols-stabilized CdTe, CdTe/CdS core-shell structured and CdTe/CdS/ZnS core-shell-shell structured QDs, with a variety of cell lines including K562 and HEK293T. We have demonstrated that the CdTe QDs are highly toxic for cells due to the release of cadmium ions. Epitaxial growth of a CdS layer reduces the cytotoxicity of QDs to a small extent. However, the presence of a ZnS outlayer greatly improves the biocompatibility of QDs, with no observed cytotoxicity even at very high concentration and long-time exposure in cells. Our systematic investigation clearly shows that the cytotoxicity of QDs can be modulated through elaborate surface coatings and that the CdTe/CdS/ZnS core-shell-shell structured QDs directly synthesized in aqueous phase are highly promising biological fluorescent probes for cellular imaging.