Since magnetic resonance imaging (MRI) technique is constantly evolving with higher field strength scanners, the question arises whether images from different field strength scanners can be used interchangeably for scientific and clinical purposes. We address this issue in a study group of patients with temporal lobe epilepsy (TLE). Two different quantification methods for analysing structural (MRI) were used. Conventional volumetry was performed by manually tracing amygdala and hippocampus volumes on both 1.5 and 3T scans of 10 TLE patients. Additionally a voxel-based morphometry (VBM)-based extraction of those structures was conducted. As an answer to the main question, it was determined that the volumetrically derived volumes of amygdala and hippocampus from 1.5 and 3.0T images did not differ. Our findings concerning the volumetry are consistent with findings in healthy controls, thus offering the possibility to use volumetry of the different scanners interchangeably. The results of the VBM-analyses show satisfying inter-scanner volume quantification but not consistent enough to be deemed interchangeable. Further investigations analysing the outcomes of conventional VBM of different field strength scanners are necessary.