Technical Abstract: Diverse procedures have been reported for the separation and analysis of secondary metabolites called capsaicinoids, pungent compounds in the fruit of various species of the Capsicum (Solanaceae) plant. To further improve the usefulness of high-performance liquid chromatography (HPLC) and liquid-chromatography/mass-spectrometry (LC-MS) methods, studies were carried out on the influence of several parameters on the analysis of extracts containing up to seven capsaicinoids. The analysis was optimized by defining effects on retention times of (a) the composition of the mobile phase (acetonitrile: 5% formic acid in H2O); (b) column length (Inertsil ODS-3v, 150 -400 mm); and (c) capacity values (k) of column packing. Identification was based on retention times and mass spectra of individual peaks. Quantification was based on the UV response in the HPLC method and on recoveries from spiked samples. The results make it possible to select analysis conditions that produce well-separated peaks associated with seven capsaicinoids extracted from pepper-containing matrices. The method (limit of detection of ~ 15-30 ng) was used to quantify capsaicinoid levels in extracts of various parts of the pepper fruit (pericarp, placenta, seeds and in the top, middle, and base parts of whole peppers); in fresh and freeze-dried peppers; and in pepper-containing foods. The results demonstrate the usefulness of the method for the analysis of a wide range of very low to very high amounts of capsaicinoids (~ 0.5 to 3000 µg/g). The described procedures should be generally useful for assessing the role of capsaicinoids in host-plant resistance, microbiology, nutrition, and medicine.