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Resveratrol (trans-3,4',5-trihydroxystilbene) and quercetin (3,3’,4’,5,7-pentahydroxyflavone) are two naturally occurring polyphenols with the potential to exert beneficial health effects. Since their low bioavailability is a major obstacle to biomedical applications, efforts are being made to improve their absorption and slow down phase II metabolism. An accurate evaluation of the corresponding levels in the bloodstream is important to assess delivery strategies, as well as to verify claims of efficacy based on in vitro results. In the present work we have optimized a simple method ensuring complete stabilization and extraction of resveratrol and quercetin from whole blood. The suitability of different protocols was evaluated by measuring the recovery of polyphenol and internal standard from spiked blood samples via HPLC/UV analysis. The optimized procedure ensured a satisfactory recovery of both internal standards and compounds. Comparing plasma and whole blood, up to 76% of the analyte, being associated with the cellular fraction, was unaccounted for when examining only plasma. This indicates the importance of analysing whole blood rather than plasma to avoid underestimating polyphenol absorption in bioavailability studies.