Quantum dots have now become the most important candidates and widely exploited as promising architectures for use as diagnostic and imaging agents in biomedicine and as semiconductors in the electronics industry. This article emphasizes on the aqueous synthesis of water soluble CdSe/CdS/ZnS core/shell/shell quantum dots with L-cysteine and mercaptopropionic acid as capping agent and their observed properties have been compared. The biocompatibility of the assynthesized quantum dots have also been analyzed through the cytotoxicity study using MTT assay. The structural, morphological and optical properties of these quantum dots have been examined through X-ray diffraction (XRD), high resolution transmission electron microscopy (HRTEM), UV-Visible absorption spectroscopy (UV-Vis) and Photoluminescence spectroscopy (PL). The capping of L-cysteine and mercaptopropionic acid on the quantum dots has been confirmed from Fourier transform infrared spectroscopy (FTIR). XRD results demonstrated the formation of hexagonal wurtzite structure for L-cysteine and cubic zinc blende structure for mercaptopropionic acid capped CdSe/CdS/ZnS quantum dots. From the optical measurements, it is observed that there is a considerable increase in the photoluminescence intensity of L-cysteine capped quantum dots than MPA. The HRTEM images revealed the narrow size distribution and in addition, L-cysteine capped quantum dots were found to be more biocompatible than mercaptopropionic acid capped quantum dots which would provide new opportunities for applications in bioimaging and biolabelling.