Anthocyanins, which are dietary flavonoids occurring in fruit and beverages, are reported to have a beneficial impact on a wide range of chronic diseases, such as cardiovascular, neurodegenerative and neoplastic diseases. To understand the underlying mechanisms, a biochemical description of the changes in cell metabolism caused by anthocyanins can be provided by metabonomic studies. The aim of this study was to detect changes in the profiles of metabolites induced by the administration of cyanidin 3-glucoside to adult male rats. A physiological dose of cyanidin 3-glucoside was intravenously administered, and blood, kidneys and liver were collected after 5 min. The tissues were rapidly frozen in liquid nitrogen, stored briefly at −80 °C, homogenised under cryogenic conditions and extracted in ice-cold methanol:water (95:5, v/v). The extracts were then analysed using UPLC/QTOF-MS. Multivariate statistical analysis of the data was performed using orthogonal projections to latent structures-discriminant analysis (OPLS-DA). Discriminating variables were compared to the in-house standard database, considering matches in retention times, parent mass ions, mass fragment patterns and isotopic patterns. This metabolomic approach made it possible to identify as many as eight metabolite markers, including bile acids, reduced and oxidised glutathione and some lipids. Such changes suggest that cyanidin 3-glucoside has a major effect on tissue antioxidant status as well as on energy and glucose metabolism.