Capillary electrophoresis has been widely used for the analysis of physiological samples such as plasma and microdialysate. However, sample destacking can occur during the analysis of these high-ionic strength samples, resulting in poor separation efficiency and reduced sensitivity. A technique termed pH-mediated stacking of anions (base stacking) has previously been developed to analyze microdialysate samples and achieve on-line preconcentration of analytes by following sample injection with an injection of sodium hydroxide. In this work, the mechanism of base stacking was investigated. Peak efficiency was shown to be a function of background electrolyte and sample ionic strength. Analytes representing several classes of compounds with a wide range of mobilities were used to study the effects of multiple parameters on sample stacking. The length of hydroxide injection required for stacking was shown to be dependent on analyte mobility and the type of amine background electrolyte used. Combinations of electrokinetic and hydrodynamic injections of sample and hydroxide were examined and it was concluded that although stacking could be achieved with several injection modes, electrokinetic injection of both sample and hydroxide was most effective for sample stacking. The mechanism of pH-mediated stacking for each of these modes is presented.