Focal cortical dysplasias type II (FCD II) are highly epileptogenic lesions frequently causing pharmacoresistant epilepsy. Detection of these lesions on MRI is still challenging as FCDs may be very subtle in appearance and might escape conventional visual analysis. Morphometric MRI analysis is a voxel-based post-processing method based on algorithms of the statistical parametric mapping software (SPM5). It creates three dimensional feature maps highlighting brain areas with blurred grey-white matter junction and abnormal gyration, and thereby may help to detect FCD. In this study, we evaluated the potential diagnostic value of morphometric analysis as implemented in a morphometric analysis programme, compared with conventional visual analysis by an experienced neuroradiologist in 91 patients with histologically proven FCD II operated on at the University Hospital of Bonn between 2000 and 2010 (FCD IIa, n = 17; IIb, n = 74). All preoperative MRI scans were evaluated independently (i) based on conventional visual analysis by an experienced neuroradiologist and (ii) using morphometric analysis. Both evaluators had the same clinical information (electroencephalography and semiology), but were blinded to each other's results. The detection rate of FCD using morphometric analysis was superior to conventional visual analysis in the FCD IIa subgroup (82% versus 65%), while no difference was found in the FCD IIb subgroup (92% versus 91%). However, the combination of conventional visual analysis and morphometric analysis provided complementary information and detected 89 out of all 91 FCDs (98%). The combination was significantly superior to conventional visual analysis alone in both subgroups resulting in a higher diagnostic sensitivity (94% versus 65%, P = 0.031 for FCD IIa; 99% versus 91%, P = 0.016 for FCD IIb). In conclusion, the additional application of morphometric MRI analysis increases the diagnostic sensitivity for FCD II in comparison with conventional visual analysis alone. Since detection of FCDs on MRI during the presurgical evaluation markedly improves the chance of becoming seizure free postoperatively, we apply morphometric analysis in all patients who are MRI-negative after conventional visual analysis at our centre.