Watercored (WC) apples, characterized by flesh that has a translucent, water-soaked appearance, have gained wide popularity with Japanese consumers. To understand this preference for WC apples, we performed a combination of sensory analysis and metabolic profiling on apple flavors using 'Fuji and 'Kotoku', cultivars susceptible to watercore. The sensory characteristics of WC 'Fuji were enhanced in aroma intensity, floral, sweet and fruity attributes compared to non-WC apples. Rating of preference was also high in WC apples. In regards to the flavor components of 'Fuji' and 'Kotoku', solubles of sorbitol, sucrose, L-alanine, pyro-glutamate and putrescine, volatiles of methyl and ethyl esters, such as methyl 2-methylbutanoate, ethyl 2-methylbutanoate and ethyl hexanoate, were significantly greater in WC apples. While the degree of sweetness with sugar composition slightly increased in a trial calculation, sweet and floral aroma presenting volatiles were remarkably elevated in the WC apples. Thus, we propose that ethyl and methyl esters, which are anaerobically-biosynthesized in the watercored area, contributed to the high preference for WC apples among Japanese consumers.