The aim of this study was to determine the phenolic components in the flowers and leaves of wild-growing Sambucus nigra L. Plant materials were collected from eleven localities in Kosovo. Before LC-DAD-ESI-MSn analysis, an ultrasonic-assisted method with 70% methanol for 30 min extraction was used. In total, 34 and 37 phenolic compounds were identified in flower and leaf extracts, respectively, with a total content of 61321.82-85961.64 mg/kg dry weight (DW) and 36136.62-93890.37 mg/kg DW. In all of the analyzed extracts, 15 phenolic acids, 20 flavonoids, one lignan, and one coumaroyl iridoid were detected. The major components were flavonoids, especially flavonols (quercetin-3-rutinoside, caffeoyl-kaempferol, and isorhamnetin-3-rutinoside), followed by phenolic acids (dicaffeoylquinic acid isomer, caffeic acid derivative, dicaffeoylquinic acid isomer, and dicaffeoylquinic acid isomer). In general, the methanolic extracts of flowers have shown higher polyphenolic content than those found in leaves. The multivariate statistical analysis of the phenolic content of the samples resulted in PLS-DA models with appropriate correlation coefficients of 0.903 and 0.921 for flower and leaf extracts, respectively. The models revealed distinctive clustering patterns, and the loading scatter plots depicted the unique phenolic compounds specific to each sample group.