Water-soluble luminescent CdS quantum dots (QDs) capped by polyphosphate, L-cysteine, and thioglycerol were synthesized in aqueous solution. The ligands were found to have a profound effect on the luminesence response of CdS QDs to physiologically important metal cations. Polyphosphate-capped CdS QDs were sensitive to nearly all mono- and divalent cations, showing no ion selectivity. Conversely, thioglycerol-capped CdS QDs were sensitive to only copper and iron ions. Similar concentrations of physiologically relevant cations, such as zinc, sodium, potassium, calcium, and magnesium ions did not affect the luminescence of thioglycerol-capped CdS QDs. On the other hand, L-cysteine-capped CdS QDs were sensitive to zinc ions and insensitive to other physiologically important cations, such as copper, calcium, and magnium ions. To demonstrate the detection capability of these new ion probes, L-cysteine and thioglycerol-capped CdS QDs were used to detect zinc and copper ions in physiological buffer samples. The detection limits were 0.8 microM for zinc (II) and 0.1 microM for copper (II) ions. The emission enhancement of the QDs by zinc (II) is attributed to activation of surface states, whereas the effective reduction of copper (II) to copper (I) may explain the emission decrease of the thioglycerol-capped CdS QDs when charged with copper ions. Unlike organic fluorescent dyes, the thioglycerol-capped luminescent CdS QDs discriminate between copper and zinc ions and are therefore suitable for the analysis of copper ions in biological samples in the presence of physiological concentrations of zinc ions. The interference of iron ions with zinc and copper ion detection is attributed to an inner filter effect, which is eliminated by adding fluoride ions to form the colorless complex FeF6(3-). To the best of our knowledge, this is first use of luminescent semiconductor quantum dots as selective ion probes in aqueous samples.