I have an autoimmune disease (Crohn's disease) and my children were perfect. For many autoimmune sufferers, pregnancy either a. makes the disease better, b. makes it worse, c. you stay the same.
They have found that the more genetically DIFFERENT your child is from you, the more likely it is that you will NOT get worse while carrying them. So, hopefully you married someone whose background (family tree) is not a carbon copy of yours. So for me, I am Irish, English, Dutch, French (x2), German and Native American (x2). My husband is Italian, Portuguese and English. Doctors told me that it was good that we genetically crossed only along English lines because it lessens the chances that my children will inherit the disease.
Good thing we American's are all immigrants (except Native Americans) and mixed heavily! From a medical perspective, it IS good to add in new immigrants from other countries to our breeding pool.
I should add though, that many autoimmune sufferers that did well in pregnancy, get very ill AFTER the birth, so it is critical to be ready to treat the disease the second you are no longer pregnant. With my second pregnancy, I stayed on Remicade and let me tell you - it was worth it! My son had a great birth weight and I did not get a flare-up after his birth. I breastfeed him on Remicade as well, which has finally been approved for both breastfeeding and pregnancy.