Genetically modified (GM) Chinese cabbage containing the bar gene was compared to 24 non-GM Chinese cabbage varieties to evaluate unwanted changes in GM crops using HPLC-DAD-based metabolic fingerprinting to characterize polar metabolites containing flavonoids. No new compounds distinguishing GM crops from non-GM crops were observed using this technique. The GM crops had the similar flavonoid value as its nontransgenic counterpart (cv. Samjin). Moreover, the luteolin, quercetin, and kaempferol contents in GM Chinese cabbage were within the range of the 24 cultivars. The metabolome database included major 26 chemical species, which were analyzed with principal component analysis. The results clearly demonstrated that the time of sampling affects the metabolome. Moreover, the metabolic fingerprints showed a range of natural variability in the GM Chinese cabbage that was similar to that of the control at all times of sampling. Metabolic fingerprinting could potentially provide an innovative method for safety assessments of genetically modified organisms.