Compounds 1-4 are diastereoisomeric thymine derivatives of isochroman aromatic analogues of stavudine, an approved drug. Both capillary electrophoresis (CE) and high-performance liquid chromatography (HPLC) techniques were used to separate these species with high resolution and thus permit the determination of enantiomeric excess. Chiral selectivity was developed using anionic (highly sulfated) cyclodextrins as chiral selectors in CE and amylose, cellulose and cyclodextrin chiral stationary phases by HPLC. The HPLC method was found to be more efficient than the CE method and was applied, after validation (repeatability, limit of detection, limit of quantification) to follow and quantify the kinetics of a stereoselective esterification.