A capillary electrophoresis (CE) method for the analysis of a sulfobutyl ether beta-cyclodextrin (SBE-beta-CD) mixture is described. The SBE-beta-CD has been prepared as a parenterally safe solubilizing agent and has historically been characterized by elemental analysis and nuclear magnetic resonance spectroscopy. While these methods provide gross values for the degree of substitution, the CE method described resolves the mixture of positional and regional isomers based on the degree of SBE substitution. The method uses benzoic acid in the running buffer and detects the CD by a decrease in background absorbance of the benzoic acid due to complexation. The necessity of a defined column was sequence between injections was evaluated. The reproducibility of migration times and peak areas/heights for 10 components of the mixture was determined. The modular CE system gave a relative standard deviation of 2.5% (n = 3) for six of the 10 peaks. Further refinements (pH buffer effects) were explored to improve the reproducibility with remaining components. The method was used to evaluate the reproducibility of the synthesis (21 different lots) and the effect of reaction variables (time, temperature and base) on the composition pattern of the modified CD.