Consumers' increasing interest in the relationship between diet and health is a sign for food producers to pay more attention to potential health-protecting compounds in new product development and food processing. From a production chain perspective the choice of the raw material that is used is important for the health-protecting potential of the end product. Four apple cultivars (Jonagold, Golden Delicious, Cox's Orange, and Elstar), which can be used as fresh apples or in processed apple products, were compared with regard to flavonol, catechins, phloridzin, and chlorogenic acid concentrations and antioxidant activity. Jonagold apples possessed the highest flavonoid concentration and the highest antioxidant activity. To study seasonal differences, apples from three different harvest years were analyzed, but in three cultivars no effect on flavonoid concentration and antioxidant activity was observed. Long-term storage, both at refrigerator temperature and under controlled atmosphere conditions, was found not to influence flavonoid concentration or antioxidant activity.