A high-performance liquid chromatography (HPLC) with diode array detector (DAD) and electrospray ionization mass spectrometry (ESI-MS) was established for the simultaneous determination of thirteen bioactive compounds in Flos Lonicerae. The optimal chromatographic conditions were obtained on a C(18) column (250x4.6 mm, 5.0 microm) with the column temperature at 30 degrees C. The mobile phase was composed of (A) acetic acid aqueous (0.4%, v/v) and (B) acetonitrile using a gradient elution, the flow rate was 1 ml/min. Detection wavelengths were set at 240 nm for iridoids (loganin, sweroside, secoxyloganin and centauroside), 330 nm for phenolic acids (chlorogenic acid, caffeic acid, 4,5-di-O-caffeoyl quinic acid and 3,4-di-O-caffeoyl quinic acid) and 360 nm for flavonoids (rutin, hyperoside, quercetin-3-O-glucoside, luteolin-7-O-glucoside and lonicerin). The identities of the peaks were accomplished by comparing retention times, UV and mass data with reference compounds under the same conditions. All calibration curves showed good linear regression (r(2)>0.9983) within test ranges. The developed method provided satisfactory precision and accuracy with overall intra-day and inter-day variations of 0.78--1.85% and 1.13--2.36%, respectively, and the overall recoveries of 91.3--104.2% for the thirteen compounds analyzed. The verified method was successfully applied to quantitative determination of the three types of bioactive compounds in ten commercial Flos Lonicerae samples from different markets in China. The analytical results demonstrated that the contents of the thirteen analytes were relatively variant.