The aim of this study was to investigate comprehensively the metabolic pathways and human bioavailability of anthocyanins and other (poly)phenols in an apple matrix, and to elucidate potential intake biomarkers. After the acute intake of a red-fleshed apple freeze-dried snack, plasma and urine were collected and analyzed by UPLC-MS/MS. A total of 37 phase-II and microbial phenolic metabolites were detected in plasma and urine. Among these, phloretin glucuronide, cyanidin-3-O-galactoside (plasma and urine) and peonidin-3-O-galactoside (urine) were the only metabolites detected in all the volunteers and not detected at basal conditions. The maximum urine excretion was detected at 2-4 h, and the main increase in plasma of phloretin glucuronide and cyanidin-3-O-galactoside was observed at 2 h post-intake (61.0 +/- 6.82 and 10.3 +/- 1.50 nM, respectively). These metabolites could be selected as the best intake biomarkers of red-fleshed apple and might be useful in human intervention studies when studying its health effects.