Without knowing which auto-immune disease its hard to give more information (which is fine, this is not medical advice). > So if I understand you correctly, th

Without knowing which auto-immune disease its hard to give more information (which is fine, this is not medical advice). > So if I understand you correctly, the self-recognition system is something built-in Yes. before immune cells are released and "primed" they go through a selection process where the receptors they have for (unknown) antigens are tested against a vast array of proteins the body normally produces, if they bind, they are killed off. Sometimes this doesn't work and if they are activated and bind their (self-)antigen when the immune system is activated (i.e. during an infection) they can attack uninfected cells. Which as a one off event is not problematic, the problem comes from the fact that those immune cells stick around when they contact their antigen, and if it is produced by the body this is a lot, and continue to kill healthy cells and cause inflammation. > and doesn't change in response to foreign antigens? By the time the immune cells bind to foreign agents they have already gone through the selection process. Necessarily a vaccine will produce an immune response (or otherwise it won't have the intended effect), this could cause an autoimmune response because the atuoresponsive cells, presumably, have their antigen around. > but this shouldn't affect the production (or culling) of T-cells that are super-sensitive to host's own self-antigens? new ones, no. In fact if you're not a child, you aren't producing many new (unique) T-cells at all. Old ones however may proliferate if their antigen is present and an immune response is triggered (to the vaccine or the virus). If you want real advice, don't take it from some random on the internet with only a minor in biomed, talk to your doctor or immunologist.