An enantiomeric assay for the flavonoids vestitone and medicarpin from transgenic plant extracts was developed using capillary electrophoresis. It was found that no single cyclodextrin proved capable of resolving the enantiomers of both medicarpin and vestitone. Instead, hydroxypropyl-beta-cyclodextrin provided the best selectivity for the vestitones while hydroxypropyl-gamma-cyclodextrin was best for the medicarpins. The addition of organic modifiers improved the resolution of both enantiomers. Acetonitrile proved best for the vestitones and only methanol improved the resolution of the medicarpins. An optimization study of mixed hydroxypropyl-beta-cyclodextrin and hydroxy propyl-gamma-cyclodextrin containing electrolytes revealed that the separation of the medicarpin enantiomers was intolerant to the presence of hydroxypropyl-beta-cyclodextrin. Our optimized running electrolyte was composed of 2 mM hydroxypropyl-beta-cyclodextrin, 20 mM hydroxypropyl-gamma-cyclodextrin, and 25 mM borate at pH 10.0 with 10% v/v methanol. This system provided a resolution of 1.47 and 1.80 for the medicarpin and vestitone enantiomers, respectively. This analysis was completed in 12 min. This separation provided a rapid screen to determine the enantiomeric purity of key flavonoids biosynthesized by transgenic legumes.