This study applies image analysis techniques and mathematical morphology and stereology approach to characterize the pore structure of mortar specimens, subjected to electrical current as simulation of cathodic protection. The purpose is to investigate the effect of electrical current flow on the development of microstructural properties in reinforced cement-based materials. In view of the significant contribution to material performance, characterization of pore microstructure in an economical and reliable way is of high relevance to permeability prediction and durability studies of cement-based materials. The pore size distribution and percolation was derived from image analysis (based on OPTIMAS software) of ESEM micrographs, captured on polished specimen sections. The methodology of applied mathematical morphology and stereological theories based on the so called ‘opening distribution’ is described and is used to calculate the pore network connectivity and thereby to estimate the permeability. The image analysis techniques are applied to mortar specimens, conditioned under the synergetic action of different stray current regimes and diverse curing environment at various hydration stages. The results reveal that apparent beneficial effects of stray current can be expected for relatively young cement-based materials which can be attributed to enhanced hydration mechanisms. In contrast, coarsening of the pore structure can be observed for a more mature matrix. Moreover this approach is compared with other general methods such as mercury intrusion porosimetry (MIP) and the comparison shows good consistency in development of parameters characterizing the materials’ microstructure.