A 33-year-old Japanese man, with a history of recurrent skin cryptococcosis, was admitted complaining of fever and severe headache for 3 weeks. He had no known risk factors for human immunodeficiency virus (HIV) infection. Cerebrospinal fluid examination revealed an elevated opening pressure of 32 cm H2O, cell counts of 884/mm3, a total protein value of 184 mg/dl, a glucose level of 16 mg/dl, and demonstrated a positive India ink stain for fungus. Cultures grew Cryptococcus neoformans. Hematological studies showed a persistently low CD4+ cell count (30/mm3) and a low CD4/CD8 ratio of 0.1. He has been repeatedly seronegative (ELISA and Western blot) for HIV-1 and HIV-2. He responded to fluconazole, and was given itraconazole as secondary prophylaxis because of persistent low CD4 counts. To our knowledge this is the first patient with idiopathic CD4+ T lymphocytopenia associated with CNS cryptococcosis in Japan. CD4 counts should be part of the initial work up for patients with CNS cryptococcosis.