Myasthenia Gravis (MG) is a neuromuscular junction disorder. It is caused by antibodies directed against the acetylcholine receptor (AchR) or Muscle-Specific Kinase (MuSK) protein. 45 years ago, researchers discovered that immunizing rabbits with AchR from an electric eel, resulted in an MG like disease. Immunizing with the AchR protein is now the usual method used to induce experimental autoimmune MG (EAMG). Development of MG is reported following the administration of many vaccines. Most cases occur following administration of the influenza vaccines per the Vaccine Adverse Event Reporting System (VAERS). A study found 20-81.2% AchR antibody level increase in 2 out of 31 patients following egg derived influenza vaccine administration and most of whom were on immunosuppressive treatment. Most influenza vaccines are manufactured using embryonated chicken eggs and contain residual egg proteins. Embryonated chicken eggs contain the chick AchR protein. We show that the chick AchR protein sequence differ from human AchR by just one or two amino acid residues. Thus they are ideally suited to activate human low affinity self reactive (LASR) T cells. These human LASR T cells that recognize human AchR with low affinity can escape the thymus due to positive selection. Such T cells with T cell receptors (TCR) that bind with high affinity to chick AchR can be activated by injected chick AchR proteins. These activated T cells interact with B cells and initiate antibody production directed against chick AchR. These antibodies cross react with human AchR to cause MG. Vaccines contain numerous animal proteins. Many of those AchR proteins are also similar to human AchR. So as above, many of these vaccines cause MG. Similar mechanism is involved in Graves’ disease (GD). Yeast (Saccharomyces cerevisiae) is used to produce recombinant Hepatitis B vaccine (HBV), Human Papillomavirus vaccine (HPV) and injectable insulin products. We show significant protein sequence homology between GD autoepitopes, animal proteins and S. cerevisiae proteins. Humoral immune response directed against S. cerevisiae occurs following HBV, HPV administration and prolonged injectable insulin usage as in type 1 diabetes. Thus leading to the development of GD and numerous other autoimmune disorders. Important findings: Animal protein containing vaccines cause autoimmune diseases even when the vaccine does not contain an adjuvant. Adjuvanted vaccines only make the problem worse. Vaccines interact to cause autoimmune diseases. Post-marketing vaccine safety surveillance systems are an abject failure.