We present a simultaneous liquid chromatographic method for the separation of two flavonoid compound families, flavanone glycosides (FGs) and polymethoxylated flavones (PMFs), which are usually found in citrus fruits species and varieties. This technique permits the quantitation of six FGs (narirutin, naringin, hesperidin, neohesperidin, didymin, poncirin) and six PMFs (sinensetin, hexamethoxyflavone, nobiletin, scutellarein, heptamethoxyflavone and tangeretin). This technique, to be used to characterize a citrus juice by its polyphenolic profile, has been applied to the determination of flavonoid compounds in grapefruit- and orange juice. Differentiation of orange juice varieties and mixtures containing tangor juice using polyphenolic profiles and flavonoid content has been achieved.