Chemical cytometry refers to the use of high-sensitivity analytical tools to characterize single cells. These tools include mass spectrometry, electrochemistry and capillary separation methods. This review focuses on the use of capillary electrophoresis coupled with high-sensitivity detection to characterize single cells. In survey experiments, biogenic amines and proteins have been characterized in single cells. In directed experiments, fluorescent substrates are used to monitor the activity of sets of enzymes, either within a family or along an enzymatic cascade. When combined with classical cytometry tools, it is now possible to monitor several cellular components in single cells as a function of cell cycle, which provides insight into the evolution of cellular composition as cells prepare for division.