Mutations in the autoimmune regulator (AIRE) gene are responsible for autoimmune polyendocrinopathy–candidiasis–ectodermal dystrophy (APECED). Systemic sclerosis (SSc) is a non-organ-specific autoimmune disease mainly characterized by cutaneous involvement, that is frequently associated with other autoimmune manifestations common to APECED. Nineteen SSc patients, 22 patients affected by SSc associated with autoimmune thyroiditis, and 100 healthy controls were analyzed. We identified 11 AIRE gene variants, one of which has never previously been described. Intronic polymorphism G11107A was significantly correlated to SSc/thyroiditis. Data show that variants of the AIRE gene might be correlated to different clinical manifestations in SSc patients.