This study presents a combined approach of establishing cultivar differences between Aegean olive oils, obtained from economically important olive oil producing cultivars (cv. Ayvalik and Memecik), based on chemometric evaluation of their content and in particular composition of the minor compounds. Evaluation of minor compounds with principal component analysis and linear discriminant analysis (LDA) indicated differentiation according to the cultivars. LDA produced a 100% correct group classification. Moreover, stigmasterol, apparent beta-sitosterol and total sterols were found to have the highest discriminating power. Memecik oils were characterized by the highest content of antioxidant compounds (alpha-tocopherol, phenolic compounds and total phenolic compounds). On the other hand, Ayvalik oil had the highest level of total sterols. The data were analyzed statistically to evaluate the differences according to variety and crop season. The minor compounds of Ayvalik and Memecik oils presented statistically significant differences (p < 0.01) according to variety, except for the hydroxytyrosol and clerosterol content. The amount of alpha-tocopherol, total phenolic compounds, apparent beta-sitosterol and total sterols varied with respect to crop season. A good correlation was observed between the amount of alpha-tocopherol, total phenolic compounds, apparent beta-sitosterol and total sterols and some climatic variables.