Nowadays, unexplained cardiovascular diseases (CVD) and heart transplant response are assessed by qualitative histological analysis of extracted endomyocardial biopsies (EMB), which is a time consuming procedure involving structural damage of the tissue and the analysis in only a few slices of a 3D structure. In this paper we propose synchrotron radiation-based X-ray phase contrast imaging (X-PCI) as a suitable technique for the analysis of different cardiac microstructures, such as collagen matrix, cardiomyocytes and microvasculature, and how they are affected in abnormal conditions. Following an established procedure in clinics, biopsies from Wistar Kyoto rats are extracted, imaged with X-PCI, and processed in order to show that the quantification of the endomysial collagen matrix, cardiomyocytes and microvasculature is possible, thus demonstrating that the intrinsic properties of X-PCI make it a powerful technique for cardiac microstructure imaging and a promising methodology for a faster and more accurate EMB analysis for CVD diagnosis and evaluation.