Chiral separation of iodiconazole, a new antifungal drug, and 12 new structurally related triadimenol analogues were studied by capillary electrophoresis with seven neutral cyclodextrins. It was found that hydroxypropyl-c-cyclodextrin (HP-c-CD) was the most effective chiral selector. Furthermore, the influence of the concentration of HP-c-CD, buffer pH, buffer concentration, temperature, and applied voltage was investigated, and the method was validated. The study of the analyte structure-enantioseparation relationships showed that substitutions in the side chains had important influences on enantiomeric separation.