Intact protein profiles established by CZE have been used to predict the cultivar of olive leaves and pulps. For this purpose, proteins were extracted using a mild enzyme-assisted extraction method, which provided higher protein recoveries and a lower environmental impact than other previously described methods. These extracts were subjected to CZE determination under basic conditions using a BGE composed of 50mM phosphate, 50mM tetraborate and 0.1% PVA at pH 9. Nine and 14 common peaks, for leaf and pulp samples, respectively, were identified in the nine cultivars studied in this work. In addition, and using linear discriminant analysis of the CZE data, olive leaf and pulp samples belonging to nine cultivars from different Spanish regions were correctly classified with an excellent resolution among all categories, which demonstrated that intact protein profiles are characteristic of each cultivar.