The aim of the study is to measure the in vitro antioxidant activity of elderberry (Sambucus nigra) fruit extract and to study its toxicity in a plant model system with regard to its possible application in food and agricultural industry. The antioxidant capacity of Sambucus nigra fruit powder was quantified by a photochemiluminescence method. The study of phytotoxicity of aqueous solutions of powder extract was performed using Allium cepa as a test organism. Photochemiluminescence determinations showed a very high antioxidant capacity of the product but also revealed its cytotoxic effect, along with mitodepressive activity and even inhibiton of mitosis at the preprophase stage when the fruit extract was used at higher concentrations. Aqueous solutions of the fruit powder have a reasonably expressed mutagenic activity in vivo on the radicles of Allium cepa, especially when they are used at a concentration of 1 g/dL for a prolonged time (48 h). At lower concentrations (0.1 g/dL), however, the mutagenic effect was not observed any more. The conclusion of our study is that Sambucus nigra fruit extract powder has a very high in vitro antioxidant activity and no mutagenic effects at low concentrations, which makes it recommendable for applications in the food industry.