The colloidal synthesis of CdSe/ZnSe core/shell quantum dots (QDs) under nitrogen gas flow is presented in this study. The optical, morphology and structural properties of CdSe/ZnSe core/shell QDs are varied by changing the growth temperature and the cadmium source (Cd2+). The Fourier transform infra‐red studies validate that CdSe/ZnSe QDs capped with functional −COOH groups were formed. The morphological and composition studies conducted using high resolution transmission microscope, selected area electron diffraction andenergy dispersive spectroscope confirmed the formation of pure and mono‐disperse QDs while photoluminescence and ultra‐violet visible spectroscopy displayed their improved fluorescent properties. Caco‐2 cell line was cultured from colon cancer and cytotoxic studies were conducted to test for cell viability of various capped 3‐MPA CdSe/ZnSe QDs at various concentrations. The formed CdSe/ZnSe QDs prominently bear the zinc‐blende structure with their particle size lying well below the Bohr excitation radii. Their hydrophilic nature and the availability of functional groups on the CdSe/ZnSe QDs makes them excellent potential labeling and therapeutic agents for the colon cancer disease diagnosis.