Enhanced understanding of diseases at the molecular level has made a paradigm shift towards identifying new biological indicators especially in nanomaterials. It is important to make Quantum Dots (QDs) more than just passive bio-probes/labels for biological imaging and cellular studies as they offers “smart” multifunctional nano-platforms. For any biomedical, optoelectronic device application, evaluation of cytotoxicity coupled with cellular uptake and internalization of QDs are imperative. This paper describes the cytotoxic studies of hydrophilic and hydrophobic QDs, capped with polyvinyl pyrrolidone (PVP) and oleic acid in human breast adenocarcinoma MCF-7, Human Embryonic Kidney (HEK-293) and Ehrlich Ascites Carcinoma (EAC) cancer cells that indicated a concentration and time dependent response in a 48 hr assay. The enhanced fluorescence emitted from the cytoplasm confirmed that the QDs were efficiently internalized by the cells. 35% cytotoxicity was observed by core-shell ZnSe/CdSe QDs in HEK-293 cells, while the hydrophobic CdSe exhibited less cytotoxicity in both MCF-7 and EAC cell lines in 48 hrs. Increased LDH leakage and decreased MTT reduction was observed in a time dependent manner. The decrease rate of LDH was found in PVP-CdSe relative to the value obtained from untreated/control cells post 24 hr. The oleic acid coating renders the core-shell CdSe QDs to be more hydrophobic thus making them less toxic due to possibly weak interaction with the cells, and low ionization of cadmium. Based on our experimental observation the sequence of cytotoxicity of tested QDs was hydrophilic greater than hydrophobic in all three cell lines.