The enantiomeric resolution of the fungicides uniconazole and diniconazole was performed using electrokinetic chromatography with cyclodextrins as pseudostationary phase (CD-EKC). A systematic evaluation of several chiral selectors was made. The anionic derivative carboxymethylated-gamma-cyclodextrin (CM-gamma-CD) was found to be the most appropriate for the enantioseparation of fungicides among all cyclodextrins tested. The influence of some experimental conditions such as nature and buffer pH, chiral selector concentration, and temperature on the enantiomeric separation of the compounds studied was also investigated. The use of a 50 mM phosphate buffer (pH 6.5) containing 5 mM CM-gamma-CD and a temperature of 50 degrees C enabled the baseline enantioresolution of mixtures of uniconazole and diniconazole in less than 5 min. In addition, apparent binding constants for each enantiomer-CM-gamma-CD pair at several temperatures, as well as thermodynamic parameters for binding were calculated.