The disease mechanism of multiple sclerosis (MS) involves inflammation, demyelination and neurodegeneration. The relation between these components is not completely understood, but recent experiences with aggressive anti-inflammatory treatment suggest that inflammation drives neuronal damage in patients with relapsing remitting MS. Although infiltration of lymphocytes into the brain parenchyma was recognized as a key event in the pathogenesis of MS more than 120 years ago, important aspects of the mechanisms triggering and sustaining this immune response remain unknown. Furthermore, studies of MS lesions and evidence from therapeutic trials suggest that the disease mechanism may vary both throughout the disease course and between patients. The understanding of MS as an autoimmune disease targeting myelin proteins is shaped by the animal model experimental autoimmune encephalomyelitis (EAE), but translation from EAE to MS has proven to be difficult. Although both the EAE model and the prominent association to HLA class II molecules suggest a key role for CD4+ T helper cells, it is not known if or how their tolerance to myelin proteins or other putative autoantigens are broken in MS. This paper reviews some important concepts and controversies in the understanding of the immunological basis for MS and its treatment.