Abstract This study was carried out in Japan for evaluation of the relationship between phenolic compounds and skin color indices of 3 apples cultivars including ‘Fuji’, ‘Jonathan’ and ‘Jonagold’, in 2006. In ‘Jonathan’, L* (lightness) increased with decreasing red color of skin. In ‘Jonagold’, chroma increased with increasing red color. But in ‘Fuji’, there was no detectable difference between these parameters and visual color change of the skin. In all three cultivars, anthocyanins and quercetins increased with increasing visible red color (decreasing L* value and hue angle). Phenolic content of the fruit pulp of studied cultivars was not related to fruit external color. Total phenolic compounds of ‘Fuji’ pulp were higher than those of ‘Jonathan’ and ‘Jonagold’. There was a significantly positive correlation between anthocyanin and quercetin 3-galactoside in all three examined cultivars. In ‘Jonathan’ and ‘Jonagold’ chroma was high in the fruits with higher content of anthocyanin, which was accompanied by higher amount of quercetin; however, this relationship was not detected in ‘Fuji’. ‘Jonagold’ peel showed higher content of flavonoids and chlorogenic acid than ‘Jonathan’ and ‘Fuji’ apples. There was no significant relationship between the skin color and pulps phenolic content of various fruits of each cultivar with different peel color. Total phenolic in ‘Fuji’ flesh was higher than that of ‘Jonathan’ and ‘Jonagold’. Analysis of correlation coefficient between skin external color and phenolics content showed that red color of peel is mainly due to anthocyanins and quercetins. Keywords: Apple, Peel color, Phenolic compounds, Anthocyanin, quercetin