Analyses of cytokinins are very important in both plant physiological and biomedical research as they are implicated in many biological processes. Reliable, sensitive, selective and inexpensive methods that are flexible and designed for automation are required for these analyses. This review addresses the advances made in the separation and determination of cytokinins by CE as well as the other applications of CE (i.e., determination of dissociation constants and complexation constants of cytokinins). The various CE modes used to separate the compounds and the quantification strategies are examined. Special attention is also focused on those aspects that improve on the sensitivity and/or selectivity, such as sample extraction and preconcentration, on-line preconcentration techniques (stacking), and/or specific detectors (e.g., MS). With the coupling to the preconcentration techniques and certain detection systems, numerous CE methods can potentially be adapted for the analysis of cytokinins in complex biological samples. Therefore, we would anticipate wider applications of CE methods in the near future for cytokinin analyses, which should facilitate a decrease in analysis cost and should help to improve analysis efficiency.