Rheumatoid arthritis (RA) is an autoimmune disorder. Rheumatoid factor (RF) and anti- citrullinated protein antibodies (ACPA) are known to play a role in RA. RF and ACPA origin is considered unknown. Vaccines contain numerous residual proteins of food, animal, plant, fungal and bacterial origin, from the manufacturing process. Protein sequence analysis shows that 14 of 14 known RF autoepitopes differ from vaccine antigens by just one amino acid residue. The immune system’s cancer surveillance system looks for exactly such antigens. Cancer begins with a single DNA mutation where one base-pair is modified. Proteins encoded by this DNA segment will therefore also exhibit a single amino acid change. So such peptides with a single amino acid change (neoantigens) are strong markers for cancer and result in an anti-cancer immune response, when accompanied by innate immune system co-stimulation. With thousands of such proteins in vaccines, there is an overwhelming anti-cancer immune response following vaccine administration. The adjuvant or live virus in the vaccine provides the requisite innate immune system co-stimulation. Since cancer cells/proteins are very similar to normal cells/proteins, attacking cancer always carries the risk of autoimmunity (collateral damage). Therefore vaccines cause numerous autoimmune diseases by triggering unnecessary anti-cancer immune responses. In the specific case of RF, the target is the immune system’s IgG antibody itself. The immune system produces IgM antibodies (RF) that bind to the IgG antibody. Since this is a case of the immune system attacking its own “soldiers” (friendly fire), it weakens the immune system’s ability to fight cancer or infections. Aluminum adjuvant in vaccines promotes citrullination of the antigens. Therefore the immune system produces antibodies against the regular and citrullinated versions of the antigen. The antibodies synthesized against citrullinated antigens (anti citrullinated protein antibodies (ACPA)) play a major role in RA. The solution is to immediately remove all non-target antigens from all vaccines and injections.