The applicability of CZE in combination with MS and MS/MS methods for the simultaneous separation and determination of 12 cytokinins was investigated for the first time. Cytokinins were first completely separated by CZE within less than 20 min using a volatile buffer and then detected directly by MS or MS/MS. Satisfactory separation of the 12 cytokinin standards was achieved using a 25 mM ammonium formate/formic acid buffer (pH 3.4) and 3% ACN v/v with a separation voltage of 25 kV. On the basis of the resolution of the neighboring peaks, the various parameters for CZE-MS optimization, such as buffer pH value, concentration of buffer and organic modifier, applied voltage and sheath liquid, were evaluated systematically. MS/MS with multiple reaction monitoring detection was carried out to obtain sufficient selectivity and sensitivity. The combination of on-line sample stacking and CZE-MS/MS achieved a detection limit in the range of 0.05-0.18 microM for the 12 cytokinins at an S/N of 3. The optimized CZE-MS/MS method was simple, rapid, low cost, robust and highly selective. Furthermore, the developed method was successfully applied to screen for endogenous cytokinins in purified coconut water extract sample. Nine cytokinins were detected and quantified in coconut water after SPE.