I want to have a baby. could having an autoimmune disease affect pregnancy?

Yes: Autoimmune disorders are more common than you would think among women. Depending on the disease, severity and the treatment of such diseases, it can affect fertility and normal pregnancies. Talk to your doctor about specific autoimmune diseases before conceiving, if possible. Be reassured that most of the time, pregnancies proceed normally for women with such diseases.

Yes, but probably no: You should be screened for anticardiolipin antibodies, especially if you have had a prior miscarriage. Also, hypothyroidism, usually caused by autoimmune thyroiditis, is a common problem, because the increased estrogen made increases thyroid binding globulin and increases your thyroid need. Have you doctor frequently check a free T3 (liothyronine) and TSH during pregnancy, if you take thyroid medication!