I was just reading about this, unfortunately the article is on my work computer, so I can't link here. I don't even remember the title at all.
Anyway, one thing that I remember specifically was that it talked about how there is evidence to suggest that there may be a link between vaccinations and autoimmune disease, although no studies proving anything either way. However the article goes on to say that once you DO have autoimmune disease, your chances of a flare-up or exacerbation of the disease are greatly increased by natural illness, and NOT by vaccination (I honestly can't remember if it differentiated live and "killed" vaccines...) So in other words, you might be smart vaccinating very carefully and deliberately if you have a history of autoimmune disease, but if you actually are diagnosed with a disease, then you absolutely should vaccinate because chances of the disease becoming worse are increased by illness moreso than vaccines.
I didn't like that thought process. It's like being backed into a corner. The vaccinations *may* be leading to increased risk of autoimmune disease, then once you have autoimmune disease, you NEED to vaccinate to protect from exacerbating the disease that the vaccines may have caused! See the circular logic? SO frustrating!
I have one son with a Primary Immune Deficiency (decreased t-cells, selective IgM deficiency, low antigen-response) and I have one son with an autoimmune disease (Celiac). Vaccine decisions are REALLY hard in this family!! I am constantly reading and researching and reading more. Ugh.
If I find the link to the article (it really was fascinating, but rather technical talking about how the antigen response works in different vaccines, and how that compares to natural immune response) I'll link to it.