In visual prosthesis research, electrically evoked potentials (EEPs) can be elicited by one or more biphasic current pulses delivered to the optic nerve (ON) through penetrating electrodes. Multi-channel EEPs recorded from the visual cortex usually contain large stimulus artifacts caused by instantaneous electrotonic current spread through the brain tissue. These stimulus artifacts contaminate the EEP waveform and often make subsequent analysis of the underlying neural responses difficult. This is particularly serious when investigating EEPs in response to electrical stimulation with long duration and multi-pulses. We applied independent component analysis (ICA) to remove these electrical stimulation-induced artifacts during the development of a visual prosthesis. Multi-channel signals were recorded from visual cortices of five rabbits in response to ON electrical stimulation with various stimulus parameters. ON action potentials were then blocked by lidocaine in order to acquire cortical potentials only including stimulus artifacts. Correlation analysis of reconstructed artifacts by ICA and artifacts recorded after blocking the ON indicates successful removal of artifacts from electrical stimulation by the ICA method. This technique has potential applications in studies designed to optimize the electrical stimulation parameters used by visual prostheses.