The aim of the study was to compare cross sections with longitudinal sections in histopathological examination of the rat heart after irradiation, to find the most optimal method for the detection of cardiac radiation injuries. For this purpose, rats were irradiated locally on the heart with a single dose of 0 or 20 Gy. At different time points after irradiation, hearts were perfused and cut into longitudinal or cross sections. In both sections, several histopathological changes were scored on a graded scale between 0 and 3. Mast cells, which are thought to play a role in tissue remodelling, were counted. After 20 Gy, frequently occurring lesions were most severe in the upper half of the ventricles and the septum. These lesions could only be detected when using longitudinal sections, resulting in a higher total histopathological score than the examination of a single cross section. From 3 months onwards, changes in coronary arteries of irradiated hearts included endothelial cell loss, a loss of smooth muscle cells and fibrosis in media and adventitia. Up to 1 month after irradiation, mast cell densities of the left and right ventricles were decreased after 15 and 20 Gy, compared to time-matched controls, followed by increases from 3 months onwards. In the left ventricle, mast cell densities correlated with myocardial degeneration and fibre loss. The results of this study show that the usage of a single longitudinal section in the histopathological examination of the irradiated rat heart leads to the recognition of more severe injuries, including myocardial degeneration and fibrosis, in ventricular tissue than the usage of a single midventricular cross section. Morphological changes observed in coronary arteries of irradiated hearts might lead to a decreased compliance of the coronary artery wall. Further investigation is needed to determine the role of mast cells in cardiac tissue remodelling after irradiation.