To gain further evidence on intra-thymic autoantigen alterations that are potentially associated with patients’ risk of developing MG, we performed a comprehensive molecular analysis of muscle—CHRNA1, RYR1, and TTN—and muscle-like—NEFM, RYR3, and HSP60—autoantigen gene expression in both follicular hyperplastic MG and thymoma thymuses, in comparison with normal control thymuses and thymomas from non-MG patients. This evidence concerns the gene CHRNA1 and thymoma.