Nanoliter-volume proton nuclear magnetic resonance (NMR) spectroscopy is used to monitor the electrolyte temperature during capillary electrophoresis (CE). By measuring the shift in the proton resonance frequency of the water signal, the intracapillary temperature can be recorded noninvasively with subsecond temporal resolution and spatial resolution on the order of 1 mm. Thermal changes of more than 65 degrees C are observed under both equilibrium and nonequilibrium conditions for typical CE separation conditions. Several capillary and buffer combinations are examined with external cooling by both liquid and air convection. Additionally, NMR thermometry allows nonequilibrium temperatures in analyte bands to be monitored during a separation. As one example, a plug of 1 mM NaCl is injected into a capillary filled with 50 mM borate buffer. Upon reaching the NMR detector, the temperature in the NaCl band is more than 20 degrees C higher than the temperature in the surrounding buffer. Such observations have direct applicability to a variety of studies, including experiments which utilize sample stacking and isotachophoresis.