X-ray microtomography (XMT) has become a popular tool for detailed investigations of a diverse range of fossils. However, XMT has not always guaranteed a satisfactory result, as the resolution of XMT images critically depends on the contrast between the fossil and its hosting rock. In this paper, XMT was applied to 11 Palaeozoic brachiopod specimens selected from a range of sedimentary rocks in order to investigate the extent of effects of mineral composition and texture in the rock and fossil shell on the quality of XMT outcomes. Our study shows that sufficient contrast in mineral composition and texture between the brachiopod shell and its infilling material is required to reproduce high-quality XMT results. Specifically, brachiopod specimens with their original calcium carbonate shell, infilled mainly with quartz grains, appear toproduce the best XMT results characterized by sharply defined shell internal structures. We also found that diagenesis is significant in determining the XMT quality. Diagenetic processes including silicification and recrystallization in the brachiopod shell and/or the infilling material generally tends to diminish the resolution of the XMT results, although this impact is considerably complicated by the degree and aspect of diagenesis. Another factor of minor significance concerns the presence of bioclasts scattered in the hosting sediment that potentially could be confused with genuine shell internal structures.