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In this study, five different black bean ( Phaseolus vulgaris L. cv. Tolosa) populations cultivated in different geographical areas including Oiartzun, Andoain, Azkoitia, San Esteban and Amasa Villabona, were studied and their polyphenolic content was determined. Two food products were prepared from the five different bean populations, cooked "Tolosa" beans and a hummus made with "Tolosa" cooked beans. Moreover, the variations of total polyphenol content (TPC), total anthocyanin content (TAC) and free radical scavenging activity by the 1,1-diphenyl-1-picrylhydrazyl (DPPH) method were analyzed for raw beans, cooked beans, and "Tolosa" beans hummus. Polyphenolic detailed composition was determined by means of HPLC-MS-QTOF analysis. The "Tolosa" bean population richest in polyphenols was selected in order to study the effect of in vitro digestion on the polyphenolic content and antioxidant effect and the degradation of the main anthocyanins was followed during the in vitro digestion. Finally, the effect of the different phases of digestion on the cytotoxicity in Caco-2 cells was determined. The results suggest that cooking "Tolosa" black beans results in an increase in the bioaccessibility of polyphenols and their antioxidant activity, which, additionally has a positive effect on Caco-2 intestinal cell viability.