Background Recent studies of profoundly deaf patients with cochlear implants have demonstrated that these patients are able to process sound in the auditory cortex in a similar way to normal subjects. However, there are large variations in outcome. Various clinical criteria are used for subject selection and the decision as to which ear is to be implanted involves electrical stimulation of the promontory which is used to confirm the persistence of auditory neurones and fibres that can be utilized by the cochlear implant. In this study we have used SPECT with Tc-99m-HMPAO to investigate activation of the auditory cortex in cochlear implantees post-surgery. In addition we also investigated whether electrical stimulation of the promontory does produce change in blood flow in the auditory cortex in pre-surgery candidates, which would indicate viable auditory networks that can be utilized by a cochlear implant device. Methods and results Image analysis was performed with SPM99. Results of a simple subtraction paradigm indicated bilateral activation of auditory cortex and Wernicke’s area in the post-implant group during auditory stimulus (speech) and bilateral activation of the ventral lateral posterior thalamus and bilateral auditory association cortex BA21/22/42, in the pre-implant group during electrical stimulus but no activation of the primary auditory cortex. A conjunction analysis used to investigate the common areas of activation across both groups during the stimulus condition showed that there was a common bilateral activation of the primary auditory cortex in both groups (BA22/41/42). In addition, analysis of a subset of the seven post-implant subjects who did not comprehend the speech in our study showed an activation (P-u < 0.05, where P-u is the peak voxel threshold, uncorrected for multiple comparisons) in the left auditory cortex that extended into area BA22 synonymous with Wernicke's area. This supports the theory that this region has a sensory role.