Background: Ablation procedures, in the context of atrial fibrillation treatment, induce lesions which are difficult to visualize in an acute phase. This study sought to develop an immunohistochemical technique to evaluate and visualize microscopically the applied acute ablation lesions, which may enable an objective assessment of the lesions as this is crucial to determine lesion transmurality. Methods: In the present study, an ablation procedure was performed in vivo in six pigs at the level of the cranial vena cava and in-vitro at the level of the ostia of the pulmonary veins using the same custom-made stents and delivery system. The antibody myosin MYBPC3 was used to visualize indirectly the denaturation process induced by the heating procedure. Subsequently, the histological images were processed by using Fiji software to make standardized sections which are objectively comparable. Results: In all samples, the ablation lesions were visualized immunohistochemically and clearly identified to enable lesion measurement. The absence of transmural lesions was noticed in the samples which were exposed to an insufficient or an extreme high energy level or in the case the myocardial layer was divided by an intermediate fat layer. Conclusions: During postmortem histopathologic evaluation of ablated tissue, this technique offers a method to specifically determine the grade of muscle protein denaturation and to assess the degree of transmurality. Moreover, this study highlights the importance of myocardial tissue shielded by connective, fat and/ or charred tissue, from the penetrating ablation heat in the context of recurrence or persistence of atrial fibrillation.