Plasma from patients with Lambert-Eaton myasthenic syndrome (LEMS), an autoimmune disease of neuromuscular transmission, contains antibodies that immunoprecipitate 125I-omega-conotoxin GVIA labeled-calcium channels solubilized from rat brain. These antibodies label a 58-kDa protein in Western blots of partially purified 125I-omega-conotoxin receptor preparations. Monoclonal antibody 1D12, produced by immunizing mice with synaptic membranes, has similar properties as these LEMS IgG. 1D12 antigen was purified by immunoaffinity chromatography and shown to bind LEMS IgG. The antigen was identified by immunoscreening a rat brain cDNA library with mAb 1D12 and found to have strong homology to the synaptic vesicle protein synaptotagmin. These antibodies immunoprecipitate calcium channels by binding to synpatotagmin, an associated protein. We suggest that the interaction between synaptotagmin and omega-conotoxin sensitive calcium channels plays a role in docking synaptic vesicles at the plasma membrane prior to rapid neurotransmitter release. Autoantibody binding to a synaptotagmin-calcium channel complex may be involved in the etiology of LEMS.