Fatty acid composition was determined for 105 virgin olive oil samples of the two dominant Cretan olive cultivars, Koroneiki and Mastoides, harvested from different producing areas at different maturity stages. The oils of the Koroneiki cultivar were characterized by lower concentrations of oleic and decaheptanoic and higher concentrations of linoleic and palmitic acids. Oils obtained from high-altitude locations were rich in monounsaturated fatty acids, while oils obtained from low-altitude locations had higher content of saturated fatty acids. Palmitic and palmitoleic acids increased with increasing altitude in both cultivars examined. The statistical analysis of the compositional data showed significant potential for the classification of the samples according to cultivar and location of origin.