Perforations (“punctae”) are one of the most characteristic morphological shell features in calcite brachiopods. The significance of punctae is that they represent discontinuities in shell biomineralisation and thus add a level of complexity that must be accounted for in any model of brachiopod shell formation. A significant hindrance to understanding punctae growth and formation is the absence of sufficient information on volume, size and density. Here, we use synchrotron-radiation X-ray tomographic microscopy (SRXTM) to obtain three-dimensional information about punctae of five species of calcite brachiopods. X-ray tomography shows that punctae morphology is species-specific and reveals previously unknown levels of complexity for each species. This information is combined with previous data on morphology to discuss the function and growth of punctae. Overall the present study demonstrates the need to increase our understanding of discontinuities and the role of cell biology in the context of biomineralisation.