Medullary bone is a fast-growing, ephemeral bone tissue found inside the bone cavities of female birds. Identifying this tissue in the bones of fossil avian and non-avian dinosaurs has the potential to determine which specimens represent reproductively mature females. However, difficulties in distinguishing medullary bone from superficially similar bone pathologies has led to uncertainty as to whether some specimens previously thought to contain medullary bone instead represent sick or injured individuals. The most frequently mentioned of these pathologies is avian osteopetrosis, a virally-induced condition in birds causing bony lesions which can resemble medullary bone. Lists of criteria, primarily using two-dimensional osteohistology, have yet to form a comprehensive framework through which all medullary bone can be positively identified, and all pathology excluded. Here, we use high-resolution computed tomography (μCT) to characterise the three-dimensional structure of medullary bone in modern birds for the first time and make comparisons to the endosteal lesions of avian osteopetrosis. We identify both qualitative and quantitative features which we suggest to be characteristic of medullary bone, including connectivity density and osteocyte lacunar orientation, and highlight conspicuously variable features which require further investigation. We find several three-dimensional which can be used to differentiate between medullary bone and avian osteopetrosis, including structural anisotropy and trabecular thickness. These three-dimensional characters can be added to the growing framework of criteria to identify medullary bone in the fossil record and thus help determine the sex of dinosaurs.