The aim of this study was to characterize the neurological dysfunction above the cele level in children with spina bifida cystica. 22 neonates were investigated prospectively to a median age of three years. Before primary closure of the spinal malformation and at three and 18 months of age, MRI and inspection of vocal cord function were performed. The children were also assessed by a physical therapist at 12 and 24 months, 19 children had a Chiari malformation, 18 children developed neurological dysfunction above the cele level. Children with signs of isolated motor impairment stabilized or improved during the second year. Six children developed severe functional impairment of respiration, feeding and motor performance within the first three months of life. Severe neurological signs/symptoms were associated with myeloschisis, clinical signs of a tethered cord and recurrent periods of shunt dysfunction.