A method based on cyclodextrin-mediated micellar electrokinetic chromatography (CD-MEKC) was developed and validated for quantification of the minor, undesired enantiomer (distomer) in the drug candidate PHA-549184, an oxazolidinone that was under development as an antibiotic. The low intrinsic solubility of the compound (0.24 mg mL−1), combined with the poor solution concentration sensitivity of capillary electrophoresis, required extensive method development to enhance the solubility of PHA-549184 while minimally degrading electrophoretic performance. A number of approaches were investigated, including inclusion of neutral and charged cyclodextrins in the background electrolyte (BGE) and addition of both charged and neutral surfactants. The final BGE contains the nonionic surfactant Brij 35: pH 2.5, 18.8 mM lithium phosphate buffer/5% highly sulfated-γ-CD/7.5 mM Brij 35. Quantitation is versus an external standard in the presence of an internal standard. The assay is selective for the distomer and proved linear with a mean recovery of 104.0% over the range 0.25–2.0%. The LOD was 0.1, and the LOQ 0.2%, both slightly higher than customary in chiral analysis, a consequence of an upper bound of 1.5 mg mL−1 placed on the sample concentration in order to maintain high efficiency for the system. Precision examined over the range 0.2–1.0% varied between 3.8% and 8.0%. No batch of drug substance registered above the detection limit for the distomer.