Mucopolysaccharidosis type II (Hunter syndrome) is an X-linked lysosomal storage disorder. A novel gross deletion in the iduronate-2-sulfatase (IDS) gene was found in a 6-year-old boy with Hunter syndrome. The phenotype of the patient was severe, including joint stiffness, kyphosis, hepatomegaly, hypertrophic cardiomyopathy, moderate mental retardation, and bilateral hearing loss. The 38.8 kb gross deletion involves exons 1-7, the proximal breakpoints lying in intron 7, at position 1307880 (GenBank NT:019686), and the distal deletion breakpoint was located at position 1346697. The large deletion correlated with the severe phenotype of this Hunter syndrome patient.