Polar metabolite profiles (amino acids, organic acids, phenols, sugars and sugar alcohols) and nonpolar metabolites (mainly fatty acids) of 11 different varieties of Onion (Allium cepa L.) bulb developed in India, were analyzed using GC-MS based metabolomics approach. PLS-DA score plot was used for visual assessments of clustering trends. The metabolites contributing for formation of segregated clustering scores were identified (p<0.05). The analyses were carried out to organize the analyzed samples in groups based on the similarities and differences in primary metabolite profiles, and to verify which metabolites accounted for maximum variability of the profiles. Distinct differences in the levels of different metabolites existed in the varieties with respect to gallic acid, organic acid, amino acid, sugar and sugar alcohol profiles. The present study suggests existence of biochemical differences in different onion varieties. Distinct clustering trends were also prominent separating varieties developed in different regions in India.