Stable, water-soluble and biologically compatible ZnSe quantum dots (QDs) with l-glutathione (GSH) as a capping agent were synthesized in aqueous medium by microwave irradiation. The GSH/Zn/Se molar ratios, reaction temperature, time and pH are the crucial factors for properties of QDs. Fluorescence (FL) spectra, absorption spectra, transmission electron microscopy (TEM), X-ray powder diffraction (XRD) and Fourier transform infrared (FTIR) spectra studies showed that the optical properties of QDs were strong, shape of QDs was similar to spherical and the particle size was about 2–3nm. The 42% quantum yield (QY) of QDs can be achieved without any post-preparative treatment. The interaction of QDs bioconjugated to bovine serum albumin (BSA) was also studied by absorption and FL spectra experiments. With addition of QDs, the FL intensity of BSA was largely quenched, which can be explained by static mechanism. The results suggested the QDs-BSA binding reaction was a static quenching.