Multiple sclerosis is a major cause of non‐traumatic neurological disability. The identification of markers that differentiate disease progression is critical to effective therapy. A combination of NMR spectroscopic metabolic profiling of urine and statistical pattern recognition was used to detect focal inflammatory central nervous system (CNS) lesions induced by microinjection of a replication‐deficient recombinant adenovirus expressing TNF‐α or IL1‐β cDNA into the brains of Wistar rats. These animals were compared with a group of naı̈ve rats and a group of animals injected with an equivalent null adenovirus. Urine samples were collected 7 days after adenovirus injection, when the inflammatory lesion is maximally active. Principal components analysis and Partial Least Squares‐Discriminate analysis of the urine 1H NMR spectra revealed significant differences between each of the cytokine adenovirus groups and the control groups; for the TNF‐α group the main differences lay in citrate and succinate, while for the IL‐1β group the predominant changes occurred in leucine, isoleucine, valine and myo‐inositol. Thus, we can identify urinary metabolic vectors that not only separate rats with inflammatory lesions in the brain from control animals, but also distinguish between different types of CNS inflammatory lesions.