During the clinical phase of bovine spongiform encephalopathy (BSE), a significant decrease was observed in the ratio of muscle glycogen to plasma L-lactic acid concentrations in BSE infected field case and experimentally infected dairy cattle compared with healthy control cattle (P<0.001), this being due to changes in the concentration of both metabolites in the BSE infected cattle compared with the control group. Furthermore, the concentration of plasma alanine was significantly increased (P<0.05) in the infected animals. No significant difference was detected between these two groups in the ratio of hepatic glycogen to plasma lactate. We infer that BSE infected cattle exhibit signs of altered energy metabolism and when applied in conjunction with changes in other metabolite biomarkers these changes may be useful for discriminating BSE infected cattle from healthy cattle or those suffering with other disorders or diseases.