What happens if taking methotrexate for autoimmune diseases?

It depends: Methotrexate is a potent immunosuppressive medication . It also helps reduce the need for corticosteroids that have significant side effects. Its major side effect is on the liver, causing liver damage; it can affect the lining of the gut; rarely it causes a hypersensitivity inflammation of the lung (Methotrexate pneumonitis). Therefore, patients need to be carefully monitored while on the drug, .

Small risk: Hopefully, what happens is that Methotrexate provides good control of the disease. Risks from Methotrexate are relatively small and include infection, reduced blood counts, hair loss, liver inflammation, allergic cough and pneumonia and possible increased risk of lymphoma.