Semiconductors quantum dots (QD) exhibit unique size-dependent optical properties which enable them to be considered for biomedical applications, including diagnosis and cancer treatment. Furthermore, the synthesis of less toxic and Cd-free QDs directly in aqueous phase assures their biocompatibility as required for nanomedicine applications. Accordingly, the present work was focused on the direct synthesis of alloyed ZnSe(S) QDs capped with thioglycolic acid (TGA) or 3-mercaptopropionic acid (MPA) in aqueous medium under microwave irradiation conditions. X-ray diffraction measurements suggested that as-synthesized QDs exhibited a solid-solution like structure with an average crystallite size of 3.8 ± 0.1 nm and 2.1 ± 0.2 nm for TGA- and MPA-capped Zn-based QDs, respectively. HRTEM measurements confirmed the small size and monodispersity of the synthesized QDs. The chemisorption of carboxy-late groups in TGA (vas COO at 1577 cm-1 and vs COO at 1388 cm-1) and MPA (vas COO at 1560 cm-1 and vs COO at 1401 cm-1) onto the QDs was confirmed by FT-IR spectroscopy analyses. The band gap energy values were estimated at 3.1eV or 3.3eV, respectively, when the QDs were synthesized in the presence of TGA or MPA species. QDs suspended in biocompatible Phosphate Buffer Saline (PBS) exhibited a remarkable photo-stability; the corresponding photo-luminescence spectra recorded under 302nm excitation evidenced strong emission peaks centered on 390nm and 395nm for TGA- and MPA-capped QDs, respectively. As-synthesized thiol-capped alloyed ZnSe(S) QDs can be considered very promising biocompatible candidates for nanomedicine applications. © 2013 Bentham Science Publishers.