Auditory evoked potentials are tools widely used to assess auditory cortex functions in clinical context. However, in cochlear implant users, electrophysiological measures are challenging due to implant-created artefacts in the EEG. Here, we used independent component analysis to reduce cochlear implant-related artefacts in event-related EEGs of cochlear implant users (n = 12), which allowed detailed spatio-temporal evaluation of auditory evoked potentials by means of dipole source analysis. The present study examined hemispheric asymmetries of auditory evoked potentials to musical sounds in cochlear implant users to evaluate the effect of this type of implantation on neuronal activity. In particular, implant users were presented with two dyadic tonal intervals in an active oddball design and in a passive listening condition. Principally, the results show that independent component analysis is an efficient approach that enables the study of neurophysiological mechanisms of restored auditory function in cochlear implant users. Moreover, our data indicate altered hemispheric asymmetries for dyadic tone processing in implant users compared with listeners with normal hearing (n = 12). We conclude that the evaluation of auditory evoked potentials are of major relevance to understanding auditory cortex function after cochlear implantation and could be of substantial clinical value by indicating the maturation/reorganization of the auditory system after implantation.