Unilateral hearing in childhood restricts input along the bilateral auditory pathways, possibly causing permanent reorganization. In this study we asked: (i) do the auditory pathways develop abnormally in children who are bilaterally deaf and hear with a unilateral cochlear implant? and (ii) can such differences be reversed by restoring input to the deprived ear? We measured multichannel electroencephalography in 34 children using cochlear implants and seven normal hearing peers. Dipole moments of activity became abnormally high in the auditory cortex contralateral to the first implant as unilateral cochlear implant use exceeded 1.5 years. This resulted in increased lateralization of activity to the auditory cortex contralateral to the stimulated ear and a decline in normal contralateral activity in response to stimulation from the newly implanted ear, corresponding to poorer speech perception. These results reflect an abnormal strengthening of pathways from the stimulated ear in consequence to the loss of contralateral activity including inhibitory processes normally involved in bilateral hearing. Although this reorganization occurred within a fairly short period ([approximately]1.5 years of unilateral hearing), it was not reversed by long-term (3-4 years) bilateral cochlear implant stimulation. In bilateral listeners, effects of side of stimulation were assessed; children with long periods of unilateral cochlear implant use prior to bilateral implantation showed a reduction in normal dominance of contralateral input in the auditory cortex ipsilateral to the stimulated ear, further confirming an abnormal strengthening of pathways from the stimulated ear. By contrast, cortical activity in children using bilateral cochlear implants after limited or no unilateral cochlear implant exposure normally lateralized to the hemisphere contralateral to side of stimulation and retained normal contralateral dominance of auditory input in both hemispheres. Results demonstrate that the immature human auditory cortex reorganizes, potentially permanently, with unilateral stimulation and that bilateral auditory input provided with limited delay can protect the brain from such changes. These results indicate for the first time that there is a sensitive period for bilateral auditory input in human development with implications for functional hearing.