Menkes disease is a rare, neurodegenerative, copper metabolism disorder characterized by mutations in ATP7A gene. Clinical symptoms include epilepsy, growth delay, reduced muscle strength, skin hyperextension, hair deformation and urologic abnormalities. However, since these clinical symptoms occur 2–3 months after birth, early diagnosis of Menkes disease is very difficult for clinicians. We report here the case of a patient who initially presented urinary tract infection followed by neurologic symptoms of Menkes disease; he was accurately diagnosed via ATP7A genetic analysis and found to harbor a novel mutation. Although neurological symptoms are the primary diagnostic feature of Menkes disease, clinicians should take into account urinary abnormalities as well, which may be an important clue to the early diagnosis of these patients.