Radiofrequency ablation is the gold standard for treating cardiac arrhythmias. However, the success rate of this procedure depends on numerous parameters. Wet lab experiments provide the opportunity to investigate cardiac electrophysiology under reproducible conditions. To evaluate the electrophysiological changes of ablated myocardium in these studies it is necessary to consider the three-dimensional (3D) geometry of the lesions. For this purpose, we investigated the usage of different magnetic resonance imaging (MRI) sequences as well as an image processing procedure to analyze in-vitro preparations. To differentiate signal intensities between nonablated and ablated tissue we evaluated FISP (fast imaging with steady-state precession; delivering dominantly T1-weighted images) and RARE (rapid acquisition with relaxation enhancement; delivering dominantly T2-weighted images). After image processing, the ablated tissue was segmented in each image slice forming a 3D volume. The geometry of the lesion was modeled by the boundary of this volume. It was generally feasible to distinguish between healthy myocardium and ablated tissue as well as to determine lesion transmurality. The analysis of the reconstructed lesion geometries from FISP and RARE MRI showed a high agreement, however T2-weighted sequences showed larger lesion volumes as well as higher variations in segmentation compared to T1- mapping. FISP with higher quality may be used to reconstruct the 3D geometry of the ablation lesions.