Alopecia areata is a common disfiguring hair loss disorder that primarily affects the hair follicle as it enters the prolonged growth phase called anagen. The last few years have yielded an explosion of more rigorously obtained data on the etiology and pathogenesis of this disorder. While a consensus is rapidly building in support of an autoimmune pathogenesis, there are still several enigmatic issues to be resolved. These include the possibility that alopecia areata is really a multientity disorder with causes that are multifactorial. This will have important implications for the research scientist's search for the jigsaw puzzle's largest missing piece--the identification of the target autoantigen(s). There is now much evidence that autoimmune diseases with both T and B cell components have shared target autoantigens/epitopes. It is likely that alopecia areata is similar, as there is now very strong evidence for the generation of autoantibodies as well as autoreactive T cells to hair follicles in the pathogenesis of this disease. The following brief review outlines the progress we have made over the last five to ten years in the characterization of hair follicle antigens targeted by antibodies in alopecia areata. Results of these studies now show that the elicitation of antibodies to hair follicle-specific proteins is a highly conserved phenomenon in all affected species studied to date. Candidate autoantigens that have been identified include the 44/46 kDa hair-specific keratin (expressed in the precortical zone of anagen hair follicles) and trichohyalin (an important intermediate filament-associated protein) expressed in the inner root sheath of the growing hair follicle. Moreover, there is evidence that anti-hair follicle antibodies are modulated during the disease process, can occur before clinically detectable hair loss, and may be reduced in titer during successful treatment. Preliminary data from passive transfer experiments suggest that in some species these antibodies may disrupt hair cycling. We are currently applying a more molecular approach (e.g., cDNA library screening) to identify hair follicle antigens truly associated with the onset of the disorder.