Mucopolysaccharidosis type II (Hunter disease, iduronate-2-sulfatase deficiency) was diagnosed in a 4-year-old female by demonstrating low iduronate-2-sulfatase activity both in leukocytes and fibroblasts and by the presence of a novel, complex rearrangement of the iduronate-2-sulfatase gene in heterozygous form. Mucopolysaccharidosis type II is inherited in an X-linked recessive manner and consequently females are rare. The disease phenotype in this case is due to complete unilateral inactivation of the nonmutant paternal X chromosome of the patient. The case presented here underscores the fact that a diagnosis of mucopolysaccharidosis type II should be suspected in any female who presents with the relevant clinical symptoms.