An increasing number of scientific studies support that flavanol-rich foods and beverages such as cocoa can promote human health, and are beneficial agents for the prevention of some diseases. Our previous studies showed that long-term cocoa intake enhances the antioxidant status in lymphoid organs and also modulates lymphocyte functionality in healthy young rats. Cocoa polyphenolic antioxidants seem to be the best candidates for those effects. However, data regarding polyphenol metabolites in tissues after a long-term cocoa intake are scarce. In the present study we mainly focus on the uptake and accumulation of epicatechin metabolites in lymphoid organs, including the thymus, spleen and mesenteric lymphoid nodes, as well as in the liver and testes after a diet rich in cocoa. Ten young weaned Wistar rats were fed randomly with a 10 % (w/w) cocoa diet or a control diet for 3 weeks, corresponding to their infancy and youth. Tissues were treated with a solid-phase extraction and analysed by liquid chromatography–tandem MS. The major compounds recovered in these tissues were glucuronide derivatives of epicatechin and methylepicatechin. The highest concentration of these metabolites was found in the thymus, testicles and liver, followed by lymphatic nodes and spleen. The high amount of epicatechin metabolites found in the thymus supports our previous findings showing its high antioxidant capacity compared with other tissues such as the spleen. Moreover, this is the first time that epicatechin metabolites have been found in high concentrations in the testes, confirming other studies that have suggested the testes as an important site of oxidation.