Systemic lupus erythematosus (SLE) was diagnosed in a 2-year-old Standardbred filly. Clinical signs of SLE included weight loss, bilateral symmetric alopecia, seborrhea, oral ulceration, and lymphadenopathy. Abnormal laboratory findings included a Coombs test-positive hemolytic anemia and positive antinuclear antibody test result. Histologic evaluation of multiple skin biopsy specimens revealed interface dermatitis with linear deposition of IgG at the basement membrane zones of the epidermis and hair follicles. The filly did not respond to glucocorticoid treatment and was euthanatized. Necropsy findings included membranous glomerulonephritis and fibrous synovitis. On the basis of these findings, SLE should be considered in the differential diagnosis of immune-mediated skin disease in horses. Definitive diagnosis of SLE relies on recognition of multisystemic disease and confirmatory histopathologic and immunopathologic findings.