Saussurea lappa (Decne.) Sch. Bip (kuth) is a well known medicinal plant of the western Himalayan region, used in oriental medicines to treat diverse complaints. In the present study, polar and non- polar fractions of ethanolic extracts of S. lappa (aerial parts and roots) were taken for detailed profiling using NMR. Fifty-six compounds of different classes were unambiguously identified with the use of 1D and 2D NMR and quantified by a relative quantification method. Metabolites belonging to diverse classes, including sesquiterpene lactones, steroids, triterpenoids, phenolics, carbohydrates, organic and amino acids were identified. Roots were enriched with sesquiterpene lactones and phenolics. Triterpenoids and steroids were dominating in the aerial parts. Biologically active sesquiterpene lactones including alantolactone, isoalantolactone, dehydrocostus lactone and costunolide were observed as 121.7±1.5, 111.7±0.6, 82.5±2.0 and 42.6±1.4 mg/g dried wt. respectively in S. lappa roots. The simultaneous presence of these four important marker compounds in the chloroform fractions of roots were the major finding of this study. Health care metabolites, myoinositol (66.97±3.0 mg/g), and choline (13.74±0.08 mg/g) were also detected in aqueous fraction of S. lappa aerial parts. NMR-based comprehensive metabolite information was used to develop the chemical signature, quality control chemical markers, and strategies to understand the chemical diversity of S. lappa.