On the basis of the fresh weight of apple fruit and its peel and the concentration of bioactive compounds, the total quantity of L-cysteine, glutathione, ascorbate, flavonols, and anthocyanins as well as phenolics was evaluated in a wide range of cultivars and two growing seasons. Apple peel as a contributor to the entire apple quantity of the examined components considerably differed in relation to the investigated compounds and was also highly cultivar dependent. A great amount of flavonols was found in apple peel (approximately 40%), followed by ascorbate (approximately 30%) and total phenolics (approximately 20%), while the lowest contribution was assessed for thiols (approximately 11% and 14% for L-cysteine and total quantity of glutathione, respectively), based on average values for both years. Seasonal variations in the quantity of antioxidants was more pronounced in apple peel, whereas the contribution of apple peel to the whole fruit was predominantly affected by the genotype. A very high positive correlation existed between apple peel and the whole fruit quantity of antioxidants.