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Binaural auditory brainstem processing was examined using evoked potential measures in 40 children who were implanted early and received a second implant simultaneously or after long or short periods of unilateral implant use. Wave latencies were shorter when evoked by the experienced versus naïve implanted ear at initial bilateral activation. Binaural difference waves were detected in most children in response to apical but not basal electrode stimulation and were prolonged in latency in children implanted after long or short delays between implants. Timing differences between the implanted ears in children receiving sequential but not simultaneous bilateral implants reflect a relative immaturity of pathways innervating the second ear and results in abnormal timing of binaural processing at this initial implant stage.