An HPLC method combined with a photodiode array detector was developed for quantitative determination of five bioactive compounds that belong to two subclasses, including limonin, phellodendrine, jatrorrhizine, palmatine, and berberine in Cortex Phellodendri. The analysis was performed on an Agilent Diamonsil C18 column (4.6 x 250 mm, 5 microm) using a gradient of acetonitrile and 0.3% aqueous diethylamine phosphate (v/v), a flow rate of 0.8 mL/min, and a detection wavelength of 220 nm. The calibration curve was linear over the range of 2.5-100.0 microg/mL for both phellodendrine and jatrorrhizine, 5.0-200.0 microg/mL for palmatine, and 7.5-300.0 microg/mL for both berberine and limonin. The average recoveries ranged from 97.56 to 102.53% with RSD < or = 1.00%. Samples from different geographical locations were analyzed to evaluate the applicability of the established method, and the results indicated that the method was efficient, sensitive, and reliable for determining limonin and four alkaloids in Cortex Phellodendri.