The aim of work was to describe methodology of surgical technique for endoluminal irreversible electroporation in the biliary tract performed within the perihilar region in porcine models. Endoluminal irreversible electroporation of the common bile duct was performed on 8 porcine models using an endoluminal device inserted during laparotomy. The endoluminal device consisted of 3 electrodes 1 cm in length, attached at 120 degrees around the balloon catheter. The procedure was conducted with following parameters: number of pulses 90, voltage of 1500 V between each couple of electrodes. Cross sectional imaging and histopathological assessment were employed for evaluations of ablation zone. Models were sacrificed in 24 hours and 96 hours after ablation. The treatment was successful in all porcine models. All animals survived the defined study period. Peri-ablation oedema within the hepatoduodenal ligament and adjacent liver tissue could be measured on post-procedural MRI or CT. Perforation in site of ablation developed in one model. Histopathological examination showed heavy regressive changes of ablated tissue. The elastic membranes of adjacent portal vein were preserved in all models. This novel endoluminal modality used within the perihilar region on porcine models is a feasible and well predictable procedure according to our experience. Further studies should explore the optimal protocol of catheter-based ablation to limit complications.