Glutaric acid (GA) and 3‐hydroxyglutaric acids (3‐OH‐GA) are key metabolites in glutaryl co‐enzyme A dehydrogenase (GCDH) deficiency and are both considered to be potential neurotoxins. As cerebral concentrations of GA and 3‐OH‐GA have not yet been studied systematically, we investigated the tissue‐specific distribution of these organic acids and glutarylcarnitine in brain, liver, skeletal and heart muscle of Gcdh‐deficient mice as well as in hepatic Gcdh^–/– mice and in C57Bl/6 mice following intraperitoneal loading. Furthermore, we determined the flux of GA and 3‐OH‐GA across the blood–brain barrier (BBB) using porcine brain microvessel endothelial cells. Concentrations of GA, 3‐OH‐GA and glutarylcarnitine were significantly elevated in all tissues of Gcdh^–/– mice. Strikingly, cerebral concentrations of GA and 3‐OH‐GA were unexpectedly high, reaching similar concentrations as those found in liver. In contrast, cerebral concentrations of these organic acids remained low in hepatic Gcdh^–/– mice and after intraperitoneal injection of GA and 3‐OH‐GA. These results suggest limited flux of GA and 3‐OH‐GA across the BBB, which was supported in cultured porcine brain capillary endothelial cells. In conclusion, we propose that an intracerebral de novo synthesis and subsequent trapping of GA and 3‐OH‐GA should be considered as a biochemical risk factor for neurodegeneration in GCDH deficiency.