We tried to investigate the incidence and the clinical profile of intractable epilepsy with hippocampal atrophy and ictal onset zones located in areas other than the hippocampus (extra-medial-temporal epilepsy; EMTE). We included patients who had hippocampal atrophy confirmed by MRI but with extra-medial-temporal ictal onset zones as verified by invasive intracranial electrodes or video-EEG monitoring. The case histories, interictal EEG, ictal semiology, other MRI findings in addition to hippocampal atrophy, and results of ictal SPECT and PET scans were evaluated. Results were compared with those of surgically proven medial temporal lobe epilepsy with hippocampal atrophy recruited during the same period. 8.5% of the intractable epilepsy patients with hippocampal atrophy had extra-medial temporal epileptogenic zones. A history of encephalitis and hemiconvulsion-hemiparesis were significantly common in the EMTE group. Most of the interictal EEGs of EMTE patients showed extratemporal irritative zones. MRI, ictal SPECT, and FDG-PET seemed to be helpful at localizing the true epileptogenic zones. The predominant EMTE seizure type was focal motor seizure with secondary generalization. Some portion of intractable epilepsy patients with hippocampal atrophy had extra-medial-temporal epileptogenic foci and careful analysis of semiology and neuroimagings could yield clues to correct diagnosis.