Abstract A capillary electrophoresis method with DAD detection has been developed and validated for ochratoxin A (OTA) determination in wine and compared with a previously validated HPLC-FL method. Although the use of UV detection has originated a high value for the quantification limit and, therefore, this method can not be used yet in the determination of OTA in wine in real samples, the analytical performance of the CE-DAD method is fully satisfactory. The more important advantage of CE is the use of the economical and ecological aqueous borate buffer in the separation process. A good correlation of the results has been obtained when 27 fortified wine samples were analyzed by CE-DAD and HPLC-FL. This work demonstrates that the CE technique is a valuable alternative to HPLC-FL analysis of OTA in wine if fluorescence detection is available.