The structure and function of the myocardial microvasculature affect cardiac performance. Quantitative assessment of microvascular changes is therefore crucial to understanding heart disease. This paper proposes the use of 3D fractal-based measures to obtain quantitative insight into the changes of the microvasculature in infarcted and non-infarcted (remote) areas, at different time-points, following myocardial infarction. We used thick slices (~100μm) of pig heart tissue, stained for blood vessels and imaged with high resolution microscope. Firstly, the cardiac microvasculature was segmented using a novel 3D multi-scale multi-thresholding approach. We subsequently calculated: i) fractal dimension to assess the complexity of the microvasculature; ii) lacunarity to assess its spatial organization; and iii) succolarity to provide an estimation of the microcirculation flow. The measures were used for statistical change analysis and classification of the distinct vascular patterns in infarcted and remote areas, demonstrating the potential of the approach to extract quantitative knowledge about infarction-related alterations.