Levels of quercetin in different parts of onion were investigated using high performance liquid chromatography (HPLC) and liquid chromatography mass spectrometry (LC/MS) suitable for use with functional food material. Two main peaks were observed on HPLC chromatograms from the extracts of the skin, and the outer, middle, and core parts of onion. Using LC/MS, peak 1 was tentatively identified as quercetin monoglucoside at m/z 466.4, and peak 2 as quercetin with [M]+ at m/z 303.3. The levels of quercetin in the skin, and the outer, middle and core parts of the plant were 16.83,2.67,0.95, and 0.35 mg/g, respectively. In the study of 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity, skin, the nonedible part, contained the highest amount of quercetin, compared to the other edible parts, and showed the highest DPPH radical scavenging activity. Levels of quercetin and DPPH radical scavenging activity increased from core to skin. All parts of onion exhibited the strongest antibacterial activity only against Staphylococcus aureus and Vibro parahaemolyticus. Antibacterial activities of onion exhibited that S. aureus was more sensitive than V. parahaemolyticus. Among the four onion extracts, the middle part showed the strongest inhibitory activity against S. aureus but all onion extracts showed similar antibacterial activities against V. parahaemolyticus.