More than 5500 people were killed in the Hanshin-Awaji earthquake disaster. Most of the neonatal intensive care units (NICU) could not offer proper services as a result of the earthquake and the Hyogo Emergency System for Neonates could not function. No one imagined that such a great disaster would occur in their home town, Kobe; however, the devastation of the quake has raised the opportunity to examine the operation of neonatal medicine in an emergency. We sent out questionnaires to perinatologists in the damaged area 2-3 months after the quake. Some hospitals in the demolished area suffered such serious damage that they could not continue work as NICU, and some in the surrounding area had problems in a number of areas, including staff, room capacity and transport methods. Under these difficult circumstances the greatest problem encountered by staff was maintaining fundamental care in NICU, that is to say keeping temperature, formula (nutrition) and prevention of infection techniques operating. In this report we discuss the effects on neonatal medicine of the earthquake in Kobe. Medical staff struggled patiently and made great efforts to recover and maintain the functioning of NICU. We believe this information will be useful for neonatology staff in other areas which may experience an earthquake in the future.