We have established cell-based assays for the improved detection of acetylcholine receptor (AChR) and muscle-specific kinase (MuSK) antibodies in myasthenia gravis. This approach has enabled us to demonstrate antibodies to “clustered” AChRs in patients who were previously AChR antibody negative and can also be used to distinguish between adult and fetal AChR antibodies in mothers of babies with arthrogryposis multiplex congenita. We summarize our recent evidence for the pathogenicity of MuSK and clustered AChR antibodies using in vivo models. Cell-based assays are now also being used for the detection of other antibodies, such as those directed to components of the VGKC/CASPR2/LGI1 complex in Morvan's syndrome, and to AQP4 antibodies in neuromyelitis optica; both of these diseases can be associated with MG and sometimes thymoma. The cell-based method is time consuming but has many advantages and may provide a gold standard for the future in the detection of pathogenic autoantibodies in patients with immune-mediated diseases.