You typically show symptoms of autoimmune attacks, like neuropathies, elevated WBCs in blood/CSF, protein in CSF, inflammation biomarkers, etc. What becomes difficult is determining what triggers the autoimmune attacks, as it could be based on diet, stress, or any range of indeterminable factors.

Providers typically are able to eliminate most of the known autoimmune diseases, but for determining a new one, you need a research team and many years.