Multiple sclerosis (MS) exhibits several clinical subtypes such as the relapsing-remitting (RR) and secondary progressive (SP) forms. In accordance with this, formation of demyelinating plaques in the central nervous system (CNS) occurs by different mechanisms. In the present study, we induced acute, biphasic and chronic (RR or SP) EAE in rats and examined the effects of decoy chemokine (7ND) gene therapy, which inhibits the migration of macrophages, to address the above issue. Interestingly, it was demonstrated that the clinical signs of acute EAE and the first attack of biphasic EAE were minimally affected, whereas chronic EAE and the relapse of biphasic EAE were completely suppressed with 7ND treatment. In the CNS, the number of infiltrating macrophages was reduced in all the stages of the three types of EAE. These findings suggest that in acute EAE and in the first attack of biphasic EAE, where anti-macrophage migration therapy was almost ineffective, pathogenic T cells are mainly involved in lesion formation. In contrast, the relapse of biphasic EAE and chronic EAE macrophages play a major role in the disease process. Thus, the mechanisms of lesion formation are not uniform and immunotherapy should be performed on the basis of information about the pathomechanisms of autoimmune diseases.