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The importance of binaural cues in auditory stream formation and sound source segregation is widely accepted. When treating one ear with a cochlear implant (CI) the peripheral auditory system gets partially replaced and processing delays get added potentially, thus important interaural time differences get altered. However, these effects are not fully understood, leaving a lack of systematic binaural fitting strategies with respect to an optimal binaural fusion. To get new insights into such alterations, we suggest a novel method of free-field auditory brainstem evoked responses (ABRs) analysis in CI users. This method does not bypass the technically induced intrinsic delays of the sound processor while leaving the whole electrode array active, thus the most natural way of stimulation is provided. We compared the ABRs collected of 12 CI users and 12 normal hearing listeners using two different stimuli (chirp, click) at four different intensities each. We analyzed the ABRs using the average of 2000 trials as well as a single trial analysis and found consistent results in the ABRs’ amplitudes and latencies, as well as in single trial relationships between both groups. This method provides a new perspective into the natural CI users’ ABRs and can be useful in future research regarding binaural interaction and fusion.