Over the past three decades, compelling evidence has emerged that the immune system can attack the nervous system with devastating consequences for human health. Either cell-mediated or humoral (antibody-mediated) autoimmune mechanisms may predominate in effecting a given disease, and either glia or neurons may fall under immune attack. A subset of these diseases has been particularly useful for understanding fundamental neuroscience as well as mechanisms of human disease. This subset involves humoral autoimmune attack on cell surface molecules subserving transmembrane signaling of excitable cells; special emphasis is placed here on proteins involved in synaptic transmission. We begin by reviewing the prototypic humoral autoimmune disease of synaptic transmission, myasthenia gravis. This provides a context for insights obtained from the study of diseases targeting molecules that regulate synaptic transmission at the neuromuscular junction and in the central nervous system. We also explore a disease where autoimmunity produces agonist antibodies acting at two distinct G-protein-coupled receptors. We conclude with an exploration of the vital issue of access of antibodies to targets within the central nervous system and the implications that such access may have in the pathogenesis of poorly understood idiopathic central nervous system diseases.