Primary cicatricial alopecias (PCA) represent uncommon inflammatory disorders that result in permanent loss of scalp hair. Cutaneous autoimmunity, most prominently chronic cutaneous lupus erythematosus (CCLE), can result in this kind of scarring hair loss. The cosmetic disfigurement caused by PCA and the very unsatisfactory therapeutic options available to date all demand a better understanding of the obscure pathobiology of PCA so as to define new therapeutic targets and strategies. Hair follicle (HF) cycling and regeneration are abolished in PCA due to irreversible, epithelial hair follicle stem cell (eHFSC) damage, triggered by major, yet unclear pro-inflammatory events (e.g. type I interferon-associated cytotoxic inflammation, loss of HF immune privilege, loss of immunosuppressive "no danger" signals). Therefore, immuno-protection of eHFSC and restitution of their immune privilege are attractive future therapeutic strategies in PCA. Chronic cutaneous lupus erythematosus-associated PCA may serve as a model system for other diseases where epithelial stem cells undergo immuno-destruction.