In this article a three-dimensional mathematical model of radiofrequency ablation during open-heart surgery is presented. It was developed to study temperature field distribution into myocardial tissue. This model uses an anatomically correct 3D model for the left atrium, obtained by magnetic resonance imaging (MRI) processing of a patient; takes into account thermoelectric characteristic differences depending on the area of electric current application; considers cooling by the air flow. An ex-vivo experiment on the pig’s heart was performed where the depth of myocardium tissue damage was measured for the model validation. It was shown that the deviation of the model data from the experiment is within the limits of instrumental measurement error. The developed model is proposed to be used for heart ablation procedures planning, or new equipment development.