A fast, selective capillary electrophoresis (CE) method was developed for piperazine counter-ion analysis and applied to the analysis of an active pharmaceutical ingredient (API) that exists as a hemipiperazine salt. Due to the poor chromophore, the detection method chosen was indirect UV detection using benzylamine as the UV absorbing probe. Piperazine quantitation was performed using diethylamine as an internal standard and the method was validated for specificity, linearity, precision, and accuracy. The results indicate the method is suitable for piperazine counter-ion analysis in support of salt form characterization.