A method for the analysis of alkaloids in Macleaya cordata (Willd.) R. Br. using high-performance liquid chromatography with diode array detection and electrospray ionization mass spectrometry (HPLC-DAD-ESI/MS) was developed. Using protopine (PRO), allocryptopine (ALL), sanguinarine (SA), and chelerythrine (CHE) as the model components, different columns for the separation and different mobile phases for the signal intensities of alkaloids in ESI/MS were investigated, respectively. The results showed that good separation and high signal intensities can be obtained on a high carbon loading (17%) reversed-phase C(18) column with 30 mM formic acid in mobile phase for the analysis of alkaloids. Under the optimal separation condition and UV detection (284 nm), linearity of the six alkaloids was obtained over concentration range from 0.05 to 100.00 microg/ml. The limit of detection (LOD) was 1.62, 1.87, 1.79, 1.76, 1.10, and 0.94 ng/ml for SA, CHE, PRO, ALL, dihydrosanguinarine (DHSA), and dihydrochelerythrine (DHCHE), respectively. The LODs with ESI/MS detection were lower three orders of magnitude than those obtained with UV detection. The proposed method could be used to control quality of the raw materials of the herb more comprehensively.