Quercetin is a major flavonoid present in onions, which acts as an antioxidant. Quercetin exists both as a free compound and conjugated with carbohydrates, primarily as glucosides in onion. Aged black onion was made through a 30 day aging process in which the onions were kept in an environment of 60℃ and high humidity (90% RH). Quercetin and quercetin glucosides were assayed in onion bulbs before and after the aging process, using high performance liquid chromatography-electrospray ion trap mass spectrometry (HPLC-ESI/MS/MS). Quercetin mono- and diglucosides were identified in fresh onion bulbs, whereas quercetin aglycone was the only form present in aged black onion bulbs. These findings indicate that the quercetin mono- and di-glucosides present in fresh onions undergo complete deglycosylation during the aging process. Such profiling will provide a rapid method that can be used to assess changes in the two major quercetin glycosides during the aging process of onion bulbs.