Actively induced Lewis rat Experimental Autoimmune Encephalomyelitis (EAE) is a highly reproducible model for portraying the acute phase of multiple sclerosis. Our aim was to get more information about this model by means of flow cytometry looking at potential markers for tracing new treatments' efficacy. Thus we characterized the changes occurring in encephalitogenic TCR Vbeta8.2(+) frequency and the adhesion molecule alpha4 integrin expression in both spleen and spinal cord T cells. The increase in both these parameters was observed only in spinal cord infiltrating T cells while relevant changes in spleen cell composition were observed as early as disease onset.