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Toxicities of CdSe and CdSe/CdS quantum dots (QDs) synthesized by ultrasound-assisted methods were investigated in vitro and in vivo. Five human cell lines were used to assess the cytotoxicity of as-prepared CdSe and CdSe/CdS by assays of MTT viability, red blood cell hemolysis, flow cytometry, and fluorescence imaging. The results show that these QDs may be cytotoxic by their influence in S and G2 phases in cell cycles. The cytotoxicity of QDs depends on both the physicochemical properties and related to target cells.