3-Mercaptopropionic acid (MPA)-capped Mn-doped ZnSe/ZnS and CdTe/CdS core/shell quantum dots (QDs) were prepared via a mild aqueous phase process. The synthesis conditions were adjusted to yield QDs with roughly similar nanocrystal average diameter and light emission wavelengths. X-ray powder diffraction, transmission electron microscopy and spectrofluorometry have been used to characterize the crystal structure and optical properties of the as-prepared QDs. Growth inhibition tests using E. coli bacterial cells were also carried out to assess the cytotoxicity of the dots and showed that core/shell ZnSe:Mn/ZnS@MPA QDs do not exhibit any cytotoxicity against E. coli cells up to a concentration of 14 μM while at this concentration CdTe/CdS@MPA core/shell QDs exert a severely more pronounced cytotoxicity. These results indicate that the cytotoxicity is likely associated to the presence of Cd in the chemical composition of CdTe/CdS@MPA QDs and that ZnSe:Mn/ZnS@MPA nanocrystals are safer and could be used as biological probes for cells and tissues imaging.