The structural characteristics of the seed-mediated synthesis of heterostructured CuS–ZnS nanocrystals (NCs) and Cu-doped ZnS (ZnS:Cu) NCs synthesized by two different protocols are compared and analyzed. At high Cu dopant concentrations, segregated subclusters of ZnS and CuS are observed. The photoluminescence quantum yield of ZnS:Cu NCs is about 50–80 %; a value much higher than that of ZnS NCs (6 %). Finally, these NCs are coated with a thin silica shell by using (3-mercaptopropyl)triethoxysilane in a reverse microemulsion to make them water soluble. Cytotoxicity experiments show that these silica-coated NCs have greatly reduced toxicity on both cancerous HeLa and noncancerous Chinese hamster ovary cells. The labeling of cancerous HeLa cells is also demonstrated. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim