Nearly all patients with repaired myelomeningoceles have an Arnold-Chiari (AC) malformation and about 20% of these patients develop clinical signs of brainstem dysfunction. The management of symptomatic AC malformation is still controversial and techniques are needed to provide an objective assessment of brainstem function. We recorded somatosensory evoked potentials (SEPs) in 52 patients aged between 8 months and 20 years (median 7.3 years) with AC malformation, to determine whether the SEPs discriminate patients with symptomatic AC malformation from those without symptoms. The subcortical far-field components P13, P14 and N18, which are generated within the brainstem, were recorded with non-cephalic reference electrodes and the cortical N20 with a frontal reference. Fourteen patients (27%) had signs and symptoms of brainstem dysfunction, which were related to the AC malformation. Abnormal SEPs were mainly recorded in symptomatic patients (sensitivity 0.7, specificity 0.9). The SEPs were particularly useful in patients from 4 years of age (sensitivity 0.9, specificity 0.9), but not in the younger age group. Abnormal somatosensory conduction reflects dysfunction of the brainstem or the upper cervical cord and may be clinically useful to assess patients with late onset symptomatic AC malformation.