Capsicum fruits contain a newly discovered phytochemical called capsinoids. Because little is known about the quantities of these compounds in both sweet and pungent pepper fruits, a high-performance liquid chromatography (HPLC) method was developed to identify and quantify the capsinoids (naturally present E-capsiate and dihydrocapsiate) utilizing fruit obtained from a variety of Capsicum spp. in the U.S. Department of Agriculture's Capsicum germplasm collection. Capsinoids were extracted with acetonitrile, filtered, and analyzed using an HPLC system equipped with a C(18) monolithic column, gradient pump, and diode array detector. The elution solvents were acetonitrile and water (60:40) with an isocratic flow rate of 1.0 mL/min. Forty-nine samples representing distinct morphotypes of four cultivated species ( C. annuum var. annuum, C. annuum var. glabriusculum, C. baccatum , C. chinense , and C. frutescens ) contained detectable levels (11-369 microg/g) of E-capsiate quantified at a wavelength of 280 nm. Nine of the E-capsiate-containing samples also had dihydrocapsiate (18-86 micro/g). Gas chromatography with a mass spectrometry detector (GC-MS) confirmed the presence of these compounds in the Capsicum spp.