The aim of this study was to extract, identify and isolate the chemical constituents of the root and leaves of Cleome viscosa by liquid chromatography coupled to electrospray ionization mass spectrometry (LC-ESI-MS). The antioxidant activity and content of associated secondary metabolites in the extracts from different parts of the plant were also measured. The free radical scavenging activity of the methanol extracts of different parts of C viscosa was determined using DPPH assays. A wide range of polar and non- polar compounds were characterized by LC-ESI-MS. Based on the obtained results, 22 and 21 compounds were characterized in the extracts of leaf and root of C viscosa, respectively. Among these compounds, cleomeolide and 57,4′.trihydroxy-6,3.5-trimethoxyflavone, in the leaf extract, and nevirapine and vincetoxicoside A, in the root extract, were considered as main compounds. Phytochemical analysis also showed that the content of bioactive compounds varied remarkably in the extract of different parts of C viscosa. The leaf ethanol extract contained higher amounts of secondary metabolites, namely total phenols and flavonoids. The antioxidant activity of the extracts was also dependent on the plant parts, which was significantly correlated with the content of bioactive compounds studied. A strong free radical scavenging activity was observed for the methanol extract of the leaf (50.3%), followed by the flower (35.2%). In general, this study confirmed a wide range of compounds in different parts of the invasive weed C viscosa, especially in the leaf, with a high free radical scavenging activity.