Abstract Cyclodextrin-modified capillary zone electrophoresis (CD-CZE) was applied successfully to the enantiomeric and isomeric separation of three herbicides (imazaquin, diclofop and imazamethabenz). Commercially available cyclodextrins were evaluated for separation of the enantiomers and isomers of the three herbicides having varied molecular structures. The enantiomers of imazaquin and diclofop, and the isomers of imazamethabenz could be resolved with a resolution of ≥1.5. The resolution was found to depend on pH of the run buffer, cyclodextrin type and cyclodextrin concentration. By employing mixed cyclodextrins in the running buffer, the three herbicides were simultaneously separated in a single run. In addition, rapid (less than 3 min) enantiomeric separation is demonstrated using imazaquin as a model herbicide. The reported capillary electrophoresis (CE) methods are simple, rapid, efficient and reproducible and our results demonstrate that CE provides a powerful analytical tool for enantiomeric and isomeric separation of herbicides.