This study aimed to clarify whether the adverse outcomes seen in babies transported between New Zealand Level III intensive care nurseries were due to the transport itself or to possible differences in care in different centres. The outcomes of 34 infants inborn at National Women's Hospital, Auckland but transported to other centres were compared with those of 68 matched controls inborn at the receiving centres and with 68 controls inborn and cared for at National Women's Hospital. Transport was associated with a transient (non-significant) deterioration in respiratory status but no increase in chronic lung disease. However, infants cared for elsewhere, whether transported or control, had more periventricular hemorrhage than Auckland babies (23% and 29% vs 15%, P = 0.03) and worse neurodevelopmental outcome (70% and 66% vs 88% of those whose outcomes were known were normal at follow up, P = 0.002). We conclude that differences in care between centres may be more important than the transport itself in determining the long-term outcome of transported neonates.