A 3-month-old male infant with cytomegalovirus infection and intractable partial seizures was treated with ganciclovir for 6 weeks. The drug was well tolerated, and virus shedding in the cerebrospinal fluid and urine was eliminated, although infantile spasms at the age of 6 months appeared. At the age of 12 months, intractable seizures persisted, and the psychomotor development of the infant was markedly delayed. To our knowledge, no previous similar case has been reported. These findings suggest that treatment with ganciclovir of infants with cytomegalovirus infection results only in cessation of virus shedding in the cerebrospinal fluid and urine without having a preventive effect on the future appearance of infantile spasms. This may be due to the irreversibility of previous brain damage from the cytomegalovirus infection and the virostatic nature of the drug.