Anthocyanins are present in human diet due to their wide occurrence in fruits and beverages. They possess antioxidant activities and could be involved in several health effects. The aim of this study was to investigate anthocyanin metabolism and distribution in the digestive area organs (stomach, jejunum and liver) and kidney, as well as a target tissue (brain) in rats fed with a blackberry (Rubus fruticosus L.) anthocyanin-enriched diet for 15 days. Identification and quantification of anthocyanin metabolites was carried out by HPLC-ESI-MS-MS and HPLC-DAD, respectively. The stomach exhibited only native blackberry anthocyanins (cyanidin 3-O-glucoside and cyanidin 3-O-pentose), while in other organs (jejunum, liver, and kidney) native and methylated anthocyanins as well as conjugated anthocyanidins (cyanidin and peonidin monoglucuronides) were identified. Proportions of anthocyanin derivatives differed according to the organ considered, with the liver presenting the highest proportion of methylated forms. Jejunum and plasma also contained aglycone forms. In the brain, total anthocyanin content (blackberry anthocyanins and peonidin 3-O-glucoside) reached 0.25 ± 0.05 nmol/g of tissue (n = 6). The urinary excretion of total anthocyanins was low (0.19 ± 0.02% of the ingested amount). Thus, organs of the digestive area indicated a metabolic pathway of anthocyanins with enzymatic conversions (methylation and/or glucurono-conjugation). Moreover, following consumption of an anthocyanin-rich diet, anthocyanins enter the brain.