HPLC separation of flavonoids and furocoumarins in the crude juices of three cultivars of Citrus bergamia Risso ("Castagnaro", "Fantastico", and "Femminello") was carried out on a C18 reversed phase column. The analysis was performed in a single run using a DAD detector coupled with an ESI-MS-MS source. Two furocoumarins (bergapten and bergamottin) were detected and quantified simultaneously with the sixteen flavonoid components previously found in industrial bergamot juice. Full characterization of the furocoumarins was performed by (1)H NMR analysis on samples separated by means of preparative HPLC. The free-radical scavenging ability of cultivar juices was assessed by using DPPH radical. The data presented show that the "Femminello" cultivar, even though it is the least common of the three, is by far the richest in health-promoting bioactive compounds (both flavonoids and furocoumarins). Given the range of applications of furocoumarins, the preparative separation described herein is proposed as a simple and rapid method to obtain this class of compounds in good yield from crude juice.