Searching for a tool to quantify motor impairment in spina bifida, transcranial and lumbar magnetic stimulation were applied in affected newborn infants. Lumbar magnetic stimulation resulted in motor evoked potentials in both the quadriceps muscle and the tibialis anterior muscle in most (11/13) subjects. However, transcranial magnetic stimulation did not lead to any response at all. A strong left-to-right correlation existed for amplitude and for latency. Lumbar magnetic stimulation proved to be applicable in newborn infants with spina bifida. Although current concepts regarding spina bifida suppose lower motor neuron dysfunction, the results of this study suggest that lower motor neuron integrity is at least partly preserved after birth. Transcranial magnetic stimulation does not lead to responses in healthy newborn infants because of insufficient synaptogenesis, myelinogenesis, and axon thickness. Therefore, conclusions on upper motor neuron function in spina bifida cannot be drawn. To what extent the method used here can achieve the aim of quantifying motor impairment is a matter of further study.