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Whether for biogeochemical studies or ocean color validation activities, high-performance liquid chromatography (HPLC) is an established reference technique for the analysis of chlorophyll a and associated phytoplankton pigments. The results of an intercomparison exercise of HPLC pigment determination, performed for the first time on natural samples and involving four laboratories (each using a different HPLC procedure), are used to address three main objectives: (a) estimate (and explain) the level of agreement or discrepancy in the methods used, (b) establish whether or not the accuracy requirements for ocean color validation activities can be met, and (c) establish how higher order associations in individual pigments (i.e., sums and ratios) influence the uncertainty budget while also determining how this information can be used to minimize the variance within larger pigment databases. The round-robin test samples (11 different samples received in duplicate by each laboratory) covered a range of total chlorophyll a concentration, [TChl a], representative of open ocean conditions from 0.045 mg m−3, typical of the highly oligotrophic surface waters of the Ionian Sea, to 2.2 mg m−3, characteristic of the upwelling regime off Morocco. Despite the diversity in trophic conditions and HPLC methods, the agreement between laboratories, defined here as the absolute percent difference (APD), was approximately 7.0% for [TChl a], which is well within the 25% accuracy objective for remote sensing validation purposes. For other pigments (mainly chemotaxinomic carotenoids), the agreement between methods was 21.5% on average (ranging from 11.5% for fucoxanthin to 32.5% for peridinin), and inversely depended on pigment concentration (with large disagreements for pigments close to the detection limits). It is shown that better agreement between methods can be achieved if some simple procedures are employed: (a) disregarding results less than the effective limit of quantitation (LOQ, an alternative to the method detection limit, MDL), (b) standardizing the manner in which the concentration of pigment standards are determined, and (c) accurately accounting for divinyl chlorophyll a when computing [TChl a] for those methods which do not chromatographically separate it from monovinyl chlorophyll a. The use of these quality-assurance procedures improved the agreement between methods, with average APD values dropping from 7.0% to 5.5% for [TChl a] and from 21.5% to 13.9% for the principal carotenoids. Additionally, it is shown that subsequent grouping of individual pigment concentrations into sums and ratios significantly reduced the variance and, thus, improved the agreement between laboratories. This grouping, therefore, provides a simple mechanism for decreasing the variance within databases composed of merged data from different origins. Among the recommendations for improving database consistency in the future, it is suggested that submissions to a database should include the relevant information related to the limit of detection for the HPLC method. [Copyright &y& Elsevier]