Eye conditions caused by autoimmune responses. Autoimmune diseases are disorders caused by a malfunctioning immune system that attacks parts of the person's own body. The eyes can be affected by many of the autoimmune diseases (e.g. rheumatoid arthritis, scleroderma and systemic lupus erythematosus) but some of them specifically target only the eyes (e.g. Mooren's corneal ulcer, cicatricial pemphigoid and some types of uveitis).