Myelin proteins of the central and peripheral nervous system range from very hydrophilic to extremely hydrophobic proteins. Their biological function and involvement in various clinically defined neurological diseases are well documented. In this review the myelin proteins will be compared with proteins of alphaviruses with emphasis on Semliki Forest Virus (strain pSP6-SFV4), to elucidate better the multiple function and the potential role in several neurological diseases. The main purpose of this review is to assist neuroscientists, neurochemists, neurologists, and other interested scientists in developing a better understanding on the information relating to myelin proteins referred in autoimmune diseases. Therefore, this review is focused on simple physiochemical background of proteins and structural aspect, which may be involved in autoimmunity. It is very unusual that few different a.a. sequences (epitops) induce indeed the same autoimmune reaction.