A capillary electrophoresis method using CDs for quality control of esomeprazole (ESO) in terms of enantiomeric purity and related substances in raw material and pellets was developed. ESO is the S-enantiomer of omeprazole (OMZ). Several parameters were evaluated, including type and concentration of buffer and CD, concentration of additives and electrolyte pH. Resolution between the enantiomers of OMZ obtained for each parameter tested was calculated and the presence of the main related substance such as OMZ sulfone was carefully monitored. The optimized system consisted of 100 mM Tris-phosphate buffer pH 2.5 with 20 mM 2-hydroxypropyl--CD, 1 mM sodium dithionite, temperature at 15 degrees C, voltage at 28 kV, and UV detection at 301 nm. Once optimized, the electrophoretic system was validated according to ICH guidelines. The limits of detection and quantification for R-OMZ were 0.6 g/mL (0.06% w/w of ESO) and 2.0 g/mL (0.2% w/w of ESO), respectively. A mean concentration of R-OMZ <0.2% limit established by the United States Pharmacopeia (USP) was found in the raw material and six-pellet samples of ESO. No other impurities were found in the samples under these conditions. Therefore, the developed method was found to be appropriate not only for enantiomeric quality control of ESO but also for the analysis of ESO and the main related substance in raw material and pharmaceutical formulations as well as for stability indicating studies.