Without the antigens being properly introduced by the MHCs, the immune cells simply ignore the antigens. So in normal hair follicles, where there is normally no, or very low, MHC expression the antigens are ignored. Once this happens the immune cells can recognize antigens unique to the hair follicle that they may have never seen before. See the Immunology section of this web site for more details on autoimmune disease and inflammatory mechanisms and read the next alopecia areata Pathogenesis II page. Indirect evidence points towards hair loss being a result of immune system activity - an autoimmune disease.
Further evidence comes from the association of alopecia areata with other autoimmune diseases.
Indirect evidence provided in support of an autoimmune mechanism is not incontrovertible. There are many theoretically possible, pathogenic pathways that may elicit hair loss in alopecia areata and lead to expression of an immune cell infiltrate. Rather, a third factor such as infection induces both hair loss and the immune response. In other words, the immune system is acting abnormally against a normally functioning hair follicle. Disease induces autoimmunity - hair follicle tissue damage or abnormal follicle activity may result in exposure of self antigens to the immune system.