This investigation reports the detection and determination of the chemical components from polar extract of the seeds and leaves of Indian Mustard i.e. Brassica juncea L. genotypes using gas chromatography-mass spectrometry (GC–MS). Many of the components in Brassica juncea L. seeds and leaves are essential for proper human nutrition as primary and secondary metabolites. The main phytochemicals identified in seeds were 2-butyl isothiocyanate (32.46%), phenylethyl isothiocyanate (28.01%), α-d-galactopyranoside (25.19%), linolenic acid (16.05%), tetradecanoic acid (11.32%) and oleic acid (15.30%). The GC–MS results clearly show that the major compounds identified in the leaves were α-methyl-d-mannopyranoside (27.18%), 2-butyl isothiocyanate (24.24%), β-d-glucopyranoside (24.54%), furaldehyde (15.96%), 1-phenyl ethanol (23.33%), ethyl benzoate (14.50%), linolenic acid (13.99%) and oleic acid (12.75%). The study confirmed that the glucosinolates with allyl and phenylethyl groups as side chain are predominant compounds in Brassica juncea L. Due to variable patterns of bioactive compounds Brassica extract could be used as natural antioxidant and source for various medicinal purposes.