To compare the diagnostic performance of 18F-FDG PET, 11C-FMZ PET, and 11C-FMZ BP imaging for the evaluation of patients with intractable partial epilepsy whose MRI findings are normal by using statistical imaging analysis. Ten patients underwent comprehensive presurgical evaluation, including PET studies, to assess the epileptic foci. The extent of cortical resection was based on the results of intracranial video-electroencephalography (IVEEG) monitoring and brain mapping under stimulation. The images of 10 patients and 30 controls were spatially normalized to templates generated in-house by non-rigid registration and the standardized images of the patients and controls were statistically compared. Epileptic focus candidates were visualized on a color map of axial images of each template and the focus site was identified in candidates for lobar location. In patients with Engel I postoperative seizure outcomes we assessed the sensitivity and specificity of the imaging methods for lobar focus localization. We also compared the concordance scores of patients with Engel I and Engel II-IV postoperative seizures. The sensitivity and specificity for lobar focus localization on 18F-FDG PET scans was 90.0% and 84.8%, respectively; it was 30.0% and 81.4% for 11C-FMZ PET, 40.0% and 66.7% for 11C-FMZ BP images, and 100.0% and 51.4% for 18F-FDG PET/11C-FMZ PET/11C-FMZ BP images. In one patient the epileptic focus not detected on 18F-FDG PET scans was shown on 11C-FMZ BP images. In patients with Engel I post-treatment seizures the concordance scores were significantly higher for 18F-FDG PET than 11C-FMZ PET and 11C-FMZ BP images (p < 0.05). With respect to sensitivity and specificity, 18F-FDG PET was superior to 11C-FMZ PET and 11C-FMZ BP imaging. However, in some patients with normal MRI results, 11C-FMZ BP studies may complement 18F-FDG PET findings in efforts to identify the epileptogenic lobar regions.