The regionalized vertebral column is a hallmark of mammalian morphology and reflects functional differentiation of the vertebral regions. Mammalian vertebrae are serially homologous and morphologically patterened by Hox expression, but also vary in number and gross morphology across species. The trabecular bone inside vertebral centra is more plastic than gross vertebral bone, and structurally adapts to better withstand forces it experiences during life. However, the functional regionalization of vertebral trabecular bone is poorly examined. Are there trabecular “regions” reflecting the differing functions and in-vivo stress patterns of gross morphological vertebral regions? Or is trabecular morphology homogeneous throughout the spine, suggesting that differences in functional demands are borne exclusively by external characteristics? To address these questions, we collected µCT scans and linear measurements of cervical, thoracic, and lumbar vertebrae in four species of large shrews, including two species of the hero shrew Scutisorex, which has a highly modified vertebral column. We compared linear measurements and trabecular bone characteristics of the cranial and caudal ends of each centrum across species. To detect unique vertebral regions, we executed principal coordinates analysis and segmented regression on three versions of our data set: trabecular bone data only, external measurements only, and the two combined. We found that some regionalization is recovered using only trabecular bone data, but trabecular bone regions do not correspond exactly to gross vertebral regions. This reflects divergence between the functional signals of internal and external vertebral bone morphology, which should be further examined in a kinematic context.