Rails are key elements in railway superstructure since these elements receive directly the train load transmitted by the wheels. Simultaneously, rails must provide effective stress transference to the rest of the track elements. This track element often deteriorates as a consequence of the vehicle passing or manufacturing imperfections that cause in rail several defects. Among these rail defects, transverse cracks highlights and are considered a severe pathology because they can suddenly trigger the rail failure. This study is focused on UIC-60 rails with transverse cracks. A 3-D FEM model is developed in ANSYS for the flawless rail in which conditions simulating the crack presence are implemented. To account for the inertia loss of the rail as a consequence of the cracking, a reduction of the bending stiffness of the rail is considered. The numerical models have been calibrated using the first four bending vibration modes in terms of frequencies. These vibration frequencies have been obtained using the Experimental Modal Analysis technique, studying the changes in the modal parameters of the rails induced by the crack and comparing the results obtained by the model with experimental results. Finally, the calibrated and validated models for the single rail have been implemented in a complete railway ballasted track FEM model in order to study the static influence of the cracks on the rail deflection caused by a load passing.