The present article describes the development and validation of an ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method for the comprehensive quantification of anthocyanin and flavonol constituents of milk-based food products. Protein precipitation by acidified methanol and ultrafiltration was utilized as sample preparation to preserve overall polyphenol composition but to eliminate milk proteins in order to comply with UPLC. Reversed-phase chromatography was optimized to achieve separation of 27 analytes in 10 min in order to reduce suppression effects, achieve a wide dynamic range, and most importantly, to resolve isomeric compounds. Positive-ion electrospray mass spectrometric detection and fragmentation of analytes was optimized, final transitions were selected for maximized selectivity, reliable quantification, and reduction of false positives. The quantitative performance of the method was validated, the main features include (1) range of lower limits of detection 0.3-30 ng/mL for glycosylated analytes, 10-300 ng/mL for aglycones, (2) lower limits of quantification 1-100 ng/mL for glycosylated analytes, 30-1,000 ng/mL for aglycones, (3) averaged intraday precision 9%, (4) calibrated range 2-180,000 ng/mL for glycosylated analytes, 60-600,000 ng/mL for aglycones, and (5) averaged accuracy 101%. Applications for yogurt and ice cream products are given. The presented data suggest that this method will help to better characterize the polyphenol composition of milk-based food products for quality control, for assessment of dietary intake, and for polyphenol bioavailability/bioefficacy studies.