We compared B cells and germinal centers in thymus from myasthenia gravis (MG) patients either with anti-acetylcholine receptor (AChR) autoantibodies or with neither anti-muscle-specific tyrosine kinase (MuSK) nor anti-AChR (seronegative MG: SN-MG). The numbers and frequencies of total and germinal center B cells varied in the SN-MG thymi, some of which were normal/atrophic. Others were clearly hyperplastic, their B cell parameters overlapping with those in AChR-positive MG, which implicates the thymus in pathogenesis. Indeed, some SN-MG patients apparently benefited from thymectomy, which should be considered a management option.