The polyphenols and total antioxidant activities of five apple cultivars, grown by organic and conventional agricultural methods in neighbouring farms, were determined and compared. Total polyphenols in the whole fruit and in the peel were determined by the Folin-Ciocalteu method, and the total antioxidant activity was determined by three established methods, diphenyl picrylhydrazyl (DPPH), azinobis (3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) and ferric reducing/antioxidant power (FRAP). Polyphenolic content for the whole fruit was in the range of 80–196 and for the peel 165–400 (mg Gallic Acid Equivalent (GAE)/100 g fresh weight) for both types of agricultural practices. Antioxidant activities of fruit extracts were also relatively similar and well correlated to their polyphenolic content. High-performance liquid chromatography (HPLC) analysis of the most important polyphenolics (chlorogenic acid, catechin, epicatechin, procyanidin B1 and B2, cyaniding 3-galactoside, phloridzin, quercetin 3-galactoside and quercetin 3-arabinoside) also showed that concentrations do not differentiate significantly between the organic and conventional apples. Statistical significance of differences in antioxidant activities among the same cultivars was relatively small (flesh + peel or peel only) for both types of apples. These results indicate that organic apples do not present higher antioxidant or nutritional value compared with conventionally grown ones, as far as polyphenolic content and total antioxidant activities are concerned.