Myelin Basic Protein (MBP) induced experimental autoimmune encephalomyelitis (EAE) in the Lewis rat, produces an an acute weakness, or paralysis of the tail and hind limb ataxia ,weakness or paralysis associated with increased permiability of the blood brain barrier, inflammation and demyelination in central nervous system (CNS). Clinical symptoms , ascending weakness or paralysis of the tail followed by the hind limbs and in rare cases the fore limbs occurs 8 and 14 days post immunisation (dpi) and is generally resolved completely by day 20 dpi. We have carried out transcriptome analysis of total RNA from the spinal cords of female Lewis rats at the peak of disease (EAE) and age matched healthy controls to identify gene expression changes associated with the disease. In these data sets we include the exon and gene expression data obtained from total RNA preparations from the spinal cords of female Lewis rats sacrificed at the clinical peak of MBP induced EAE and age matched , untreated, healthy controls. This data was used to obtain 2265 mapped IDS wich identified 1190 known genes which were differentially expressed in the spinal cord in EAE compared to healthy animals. 8 total RNA samples were prepared. A two way ANOVA comparison carried out in Partek Genomics Suite was used to detect gene transcripts for which the expression levels varied significantly (un-adjusted p-values ≤ 0.05) from the healthy controls. 2265 mapped IDs were uploaded to the Ingenuity pathway analysis suite (IPA) where 1190 known genes were identified as being differentially regulated between groups. An FDR ≤ 5% and fold change limit of +/- 4.0 further refined the data set to identify the 72 most highly and significantly differentially regulated genes in the spinal cord at the clinical peak of disease in MBP induced EAE in the Lewis rat.