Over the past decade, studies of the atomic structure and the structural mechanism of nicotinic acetylcholine receptor (AChR) gating have reached an advanced stage. AChRs are members and prototypes of the superfamily of Cys-loop pentameric ligand-gated ion channels. AChRs are expressed by neurons throughout the central and peripheral nervous systems and also by many nonneuronal cell types all over the body. Although many different AChR subtypes formed by various combinations of 17 AChR subunits exhibit distinct distribution patterns, various functional properties, and diverse pharmacological characteristics, all subunits are highly homologous and share the same topographical features as subunits of other Cys-loop receptors. Here, focusing on the antigenic structure and functional structure of muscle AChRs, we describe how the antigenic structure of muscle AChRs accounts for the pathological mechanisms by which neuromuscular transmission is impaired in myasthenia gravis. This is contrasted with the antigenic structure of a neuronal AChR involved in autoimmune dysautonomia. We also summarize AChR mutations identified in muscle AChR subunits in myasthenic syndromes. This is contrasted with disease-causing mutations revealed in neuronal AChR subunits.