Development of green based synthesis of nanoparticles has been regarded as a novel and safe alternative method compared to conventional methods. Semiconductor cadmium sulfide quantum dots (CdS QDs) possess unique biological and medical applications includes labeling cells, diagnosing of diseases and imaging intercellular events. The present paper reports the biosynthesis of CdS QDs through aqueous extracts of the regenerated hairy roots of
Rhaphanus sativus L.as the organic source for both reducing and stabilizing of Cd and S precursor ions. The characterization of synthesized QDs showed maximum absorbance peak of 460 nm and fluorescence spectrum of cadmium sulfide at 530 nm. The results of Transmission Electron Microscope (TEM) and EDS analysis demonstrated that the particles were morphologically spherical with size distribution between 2–7 nm and confirmed presence of CdS QDs. Fourier transform infrared spectroscopy (FT-IR) also showed the active presence of aromatic, amino, and carboxyl groups on the surface of quantum dots. Cytotoxicity effect of the synthesized CdS QDs on two cell lines include MCF-7 breast cancer and AGS gastric cancer were assayed through MTT assay. The results showed significant inhibitory effects of synthesized QDs on treated cells in a dose dependent manner. It was also concluded that CdS QDs had more apoptosis effect on MCF-7 cells rather than AGS cell lines. The obtained results clearly illustrated that the synthesis of CdS quantum dots with standard features would be possible through cost-effective, reliable, environmentally friendly and less toxic alternative method compared to chemical and physical processes and the MTT toxicity assay also illustrated the significant apoptotic effects of synthesized CdS QDs on carcinogenesis.