Cadmium selenide quantum dots (CdSe QDs) were synthesized in aqueous phase by the freezing temperature injection technique using different capping agents (viz. thioglycolic acid, 1-thioglycerol, L-cysteine). Absorption spectra of CdSe QDs exhibited a blue shift as compared to its bulk counterpart, which is an indication of quantum confinement effect. The photoluminescence spectra of CdSe QDs confirmed that the particles are poly-dispersed and possess enhanced luminescent property, depending upon the chemical nature of capping agents. The QDs have been characterized by Fourier-transform infrared spectroscopy, atomic absorption spectroscopy and transmission electron microscopy. Further, antimicrobial activity of as-prepared QDs has also been investigated using the disk diffusion method.