The cis (Z) and trans (E) isomers of clomiphene were separated using capillary electrophoresis. Various derivatives of cyclodextrins (CDs) were applied as buffer additives, achieving a resolution of greater than 18. The effect of various parameters, type and concentration of CDs, type and concentration of background electrolytes (BGEs), pH, and organic modifiers has been studied systematically. Migration reversal was observed in several cases. The loadability of the various buffer systems was also taken into account.