A method of calibrating stimulation threshold levels of a cochlear implant, comprises sending a series of stimulation signals having a predetermined length in time to a selected subset of a plurality of stimulation electrodes of the cochlear implant of a user, wherein for each signal of the series of stimulation signals, the stimulation level is larger compared to the stimulation level of the previous stimulation signal; receiving an electrophysiological signal for each stimulation signal from a measurement electrode attached to the head of the user; calculating a cross-correlation signal for each of the received electrophysiological signals for each stimulation level following the first stimulation signal with respect to the first electrophysiological signal received for the first stimulation signal, determining, whether the respective cross-correlation signal exceeds a predetermined threshold level, wherein the sending of the series of stimulation signals is stopped and the stimulation level is set as the threshold stimulation level for the selected subset of stimulation electrodes, in case it is determined that the cross-correlation signal exceeds the predetermined threshold level for a first time, and outputting the level of stimulation at which the sending is stopped.