Elderberry (Sambucus spp.) juice contains a variety of polyphenols, mostly anthocyanins. In order to understand the variation of polyphenol levels by genotype, various elderberry juice samples were analyzed for total phenolics (TP), total monomeric anthocyanins (TMA) and individual anthocyanin content. The Folin-Ciocalteu total phenolic method and pH differential method were used to measure the TP and TMA content, respectively. The TP and TMA concentrations of elderberry were found to vary greatly among different genotypes. TMA content varied from 2.1% for 'Sperandio' to 60.6% for the 'Bob Gordon' cultivar. In addition, ultra-performance liquid chromatography with triple quadrupole mass spectrometry was used to separate and detect individual anthocyanins from samples prepared by solid phase extraction. Multiple-reaction-monitoring was used to process data for the reduction of false positives, maximizing selectivity, and reliable quantification. The quantitative performance of the method was validated, and a detection limit of 0.3 ng-ml-1 for cyanidin 3-O-glucoside was determined. This newly developed method may serve to characterize and profile various anthocyanins in elderberry juices for quality control, assessment of dietary intake, and anthocyanin-based biomedical studies.