We describe a patient with systemic lupus erythematosus (SLE) and antiphospholipid antibody syndrome (APLS) who developed a plaque-like lesion around the mouth and lost all body hair. Biopsies of the circumoral lesion and scalp, were originally reported as containing extensive basal cell carcinoma, but on review, both showed the typical appearance of a benign malformation of the hair follicle known as basaloid follicular hamartoma. Regrowth of hair and partial resolution of the peri-oral plaque occurred with more aggressive treatment of her SLE, but the basaloid follicular hamartomas in her scalp skin persisted. There is a known, but rare, association between this pattern of basaloid follicular hamartoma, alopecia and myasthenia gravis, but only two cases have been described in association with SLE and none with APLS.