Core sampling campaigns from exploration wells are time-consuming, expensive and the capacities for core extraction are therefore limited. Furthermore, mostly reservoir sections are in the focus of investigation, while the overlying cap rock was previously often not con-sidered in the sampling strategy. Another challenge for cap rock studies is posed by the instable character of mudstones and shales. While consolidated reservoir sandstones are in most cases extractable without major structural alteration, the fine-grained and usually clay mineral-rich top seal intervals are considerably more prone to mechanical and chemical al-teration which starts immediately after recovery to the surface and extraction of the sam-pled core interval from the liner. Usually, the bulk sample material is then stored under air exposure in core sheds, potentially increasing the degree of alteration significantly. Never-theless, stored core material is in many cases the only option to gain any information about the physical properties (e.g., porosity distribution) of a mudstone top seal, and therefore the suitability of sample material for pore structural characterization after long-term storage under air exposure is of great interest in this context. This study addresses the questionable suitability of long-term stored (“stored”) sample ma-terial for pore space analyses and aims at a validation of the use of such material for further cap rock investigations. In order to assess pore space characteristics and their alteration, comparative broad ion beam – scanning electron microscopy (BIB-SEM) analyses were conducted on three sub-sets of Pannonian mudstone core samples from a burial depth of ~ 530 m. The three sample sets included i) fresh waxed core slabs from a recently drilled well, ii) plugs drilled from the same fresh core material that were subsequently preserved from air exposure, and iii) long-term stored core slabs from the same stratigraphic in-terval penetrated at equal burial depth by a nearby well that was drilled in 1970. The com-parison of pore size and geometry distributions in the range between 30 nm and ~ 2 µm offered the possibility to test the impact of different preservation and preparation states on the pore space. The BIB-SEM data reveal that pore characteristics of all three investigated sample sets are in a comparable range. The stored samples are microstructurally relatively intact and not systematically altered in comparison to the fresh core material over the quantified pore size range. Although an apparently higher frequency of µm-scale drying cracks appears in stored cores, the overall comparability of total porosity values, pore size distributions, as well as pore geometry distributions suggests that representative BIB-SEM data can even be extracted from long-term stored core samples. A slight shift towards systematically in-creased total porosity was only observed for the fresh sub-set that was subjected to plug drilling. Therefore, even under optimum conditions and for well-preserved samples, the plug preparation may have induced a certain mechanical damage. This is supported by a semi-quantitative grain size estimation based on large area overview image maps, which does not support a primary sedimentary cause for the elevated porosity values. Neverthe-less, the overall pore characteristics remained in a comparable range, highlighting that BIB-SEM seems to capture relatively undisturbed matrix properties. In summary, the results point to the validity of the applied image-based porosimetry approach, assuming that the cores show at least a certain macroscopical integrity.