To compare the sensitivities of MRI, FDG-PET and ictal/SPECT in localization of the epileptogenic substrate in patients with refractory temporal lobe epilepsy. This study included 137 patients who received surgical treatment for intractable epilepsy. MRI, FDGPET and ictal 99mTc-HMPAO SPECT were retrospectively reviewed regarding their sensitivity in lateralization of the epileptogenic zone compared to video/EEG, pathological results and surgical outcome. 104 MR-positive and 33 MR-negative patients were enrolled. In the MR-positive group, MRI, PET and ictal/SPECT were concordant to video/EEG in 72%, 83% and 73%, respectively. When compared to pathological diagnosis, they correctly lateralized the epileptogenic zone in 70%, 87%, and 73%, respectively. In patients with good surgical outcome, they correctly localized the epileptogenic zone in 79%, 88%, and 78%, respectively. In the MR-negative group, PET and ictal/SPECT were concordant with video/EEG in 82% and 58%, respectively and matching with pathological diagnosis in 85% and 56%, respectively. PET is the most sensitive method in lateralization of the epileptogenic substrate. The use of MRI, PET and ictal/SPECT as a multimodality approach improves lateralization of the affected zone particularly in cases with negative MR findings and distinguishes patients who will benefit from surgery.