Dwarf elder (Sambucus ebulus L.) is a popular medicinal plant, used for centuries in the folk medicine of the Balkan Peninsula. S. ebulus preparations have shown anti-inflammatory, anti-neoplastic and antimicrobial properties, besides abundant wound healing, antioxidant and anti-ulcerogenic activities. We developed a scheme for isolation of individual compounds utilizing different chromatographic techniques, while the structure elucidation was performed by means of 1D and 2D NMR. Five flavonoid glycosides, e.g. quercetin-3-O-laminaribioside [1], isorhamnetin-3-O-laminaribioside [2], quercetin-3-O-rutinoside [3], isorhamnetin-3-O-rutinoside [4], isorhamnetin-3-O-glucoside [5], were identified accordingly. Compounds 1 and 2 are reported for the first time in the genus Sambucus. Several triterpenes – ursolic, oleanolic and maslinic acid – were tentatively identified by GC–MS. The evaluation of anti-herpes simplex virus type 1 and antioxidant (in ORACFL and HORACFL) properties suggests that the dwarf elder fruits might serve as a powerful source of valuable molecules for various purposes.