Gradient core-shell Zn-Cu-In-S/ZnS quantum dots (QDs) of small size and with highly efficient photoluminescence were synthesized via a multi-step high-temperature method involving cation exchange. The procedure starts with the preparation of indium sulfide nanoparticles followed by the addition of Cu and Zn precursors. At this stage, Zn replaces Cu atoms and as a result the concentration of Cu ions in the final QDs is only about 5% of the total In content in a QD. Zn incorporation and the formation of a gradient ZnS shell dramatically increases the photoluminescence quantum yield. Furthermore, the formation of the ZnS shell improves the chemical stability of Cu-In-S QDs, as demonstrated by the preparation of polystyrene-QD composites and labeling of glioma cells. This work provides an effective strategy for obtaining efficient and stable fluorophores free of heavy metals.