Keratoconus is a progressive non-inflammatory corneal ectasia. Alopecia areata is complete loss of hair patches on the hairy areas of the body in association with some ocular manifestations such as cataract, or disorders of the conjunctiva, iris, lens, choroid and retina pigment epithelium. A ten-year-old patient with atopic keratoconjunctivitis, keratoconus and alopecia areata is presented. This patient has also been receiving treatment for Hashimoto thyroiditis (chronic lymphocytic thyroiditis) for more than three years. The possible association of keratoconus with multisystem autoimmune disease is discussed.