Otoacoustic emissions (OAEs) coupled with auditory brainstem responses (ABR) can help differentiate central, sensorineural, and conductive hearing losses. Pinnipeds with moderate bore canals are good OAE candidates, but OAE utility for assessing marine mammal inner ear health is not known. We examined three juvenile harbour seals (Phoca vitulina) with ear disease with computerized tomography (CT), OAE, and ABR. Combining CT, OAE, and ABR allowed simultaneous ear pathology documentation, quantification, and intracanal probe microphone position determination. Hearing was tested bilaterally from 500 Hz to 15 kHz. CT/OAE/ABR results were assessed independently. In two animals, CT showed middle ears occluded with fluid but normal auditory nerve anatomy, suggesting short-term circumscribed infection with no retrograde neuronal loss. OAE found moderately elevated response levels consistent with conductive hearing loss. ABR confirmed normal brainstem functioning. In the third animal, no OAEs or ABRs were obtainable up to 70 dB re 1 mu Pa, suggesting retrograde loss through brainstem level. CT for this animal showed inner, middle, and external ear occlusions consistent with aggressive, long-term disease. These data show volume and site of auditory pathologies are strongly correlated with OAE results in pinnipeds.