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Herbal medicines have gained global importance with both medicinal and economic implications these days. The scientific assessment has become a prerequisite for acceptance of health claims. Allium cepa is one of the richest source of flavonoids and organosulphur compounds. Wide spectrum of biological activities makes A.cepa a potential therapeutic agent. This book deals with optimization of physico-chemical parameters of skin and bulb of Allium cepa.the comparison of quercetin was carried out between skin and bulb of Allium cepa. The extraction of flavonoids was carried out by employing Soxhlet extraction method. As fermentation enhances the contents of active components in oriental drugs, the skin of Allium cepa was fermented with Aspergillus Kawachii. The fermented methanolic extract of skin of Allium cepa have great potential as antibacterial activity and can be used in the treatment of infectious diseases caused by resistant microorganisms.