Objective: Quantum dots (QDs) have been gaining popularity due to their potential application in cellular imaging and diagnosis, but their cytotoxicity has not been fully investigated. Studies about this subject are the most important investigations for using these nanoparticles in medical applications. This study aimed to evaluate the cytotoxicity effect of CdSe: ZnS on kidney and liver in embryo. Materials and Methods: 10, 20 and 40 mg/kg doses of CdSe:ZnS QDs were injected to some female mice in day 8 gestation. Structural and optical properties of QDs were studied by X-Ray Diffraction (XRD), Scanning Tunneling Microscopy (STM). Results: Histological studies of liver, kidney tissues in adult offspring showed high toxicity of CdSe:ZnS especially in 40 mg/kg dose which followed by degeneration in the cytoplasm and nucleus material in liver and degeneration of kidney tissue especially glomerular hypertrophy in a dose-dependent way. Conclusion: On the whole, this study showed high toxicity of CdSe:ZnS on liver, kidney tissue, even in lower doses. Lately, QDs have been considered for photodynamic therapy of cancer. Considering results of this study about high toxicity, destruction in nuclear matter and their specific binding to the target, it seems that studies in this category can be very promising. Considering the lack of literature review in this field, this study can be an introduction to researches about histopathological effect of QDs on various organs.