This article highlights the utility of micro-computed tomography (micro-CT) for characterisingmicroscale bone morphology. For this purpose we tested selected samplesof the human bones (Wormian bone, rib, lumbar vertebra) to reconstruct externaland internal morphological features. Selected bony samples were investigatedusing a micro-CT scanner (Skyscan 1172, N.V., Aartselaar, Belgium). The imageresolution of scans varied from 5 to 27 μm/pixel depending on the bone sample.We used CTvox software (by Skyscan) to perform volume rendering of the samples.Further, 3-dimensional geometrical models were reconstructed using theCTvol application. Such models enabled graphical distinction between osseouscomponents of various morphology and were used to visualise the Haversian canalsystem inside the compact bone of the rib. Applying a modified transfer functionfor volume rendering we presented the overall morphology of the Wormian boneand small vascular channels penetrating its interior. As an example of quantitativeanalysis based on micro-CT scans we compared the trabecular structure of thelumbar vertebrae with CTAn software. Significant differences in percent bonevolume (BV/TV) were determined. Micro-CT was found to be a very accurate andhelpful method to study small anatomical structures of the bones in micro scale.