Micro-CT is a non-destructive technique for 3D tomographic investigation of an object. A 3D representation of the internal structure is calculated based on a series of X-ray radiographs taken from different angles. The spatial resolution of current laboratory-used micro-CT systems has come down over the last years from a few tens of microns to a few microns. This opens the possibility to perform histological investigations in 3D on a virtual representation of a sample, referred to as virtual 3D histology. The advantage of micro-CT based virtual histology is the immediate and automated 3D visualization of the sample without prior slicing, sample preparation like decalcification, photographing and aligning. This not only permits a drastic reduction in preparation time but also offers the possibility to easily investigate objects that are difficult to slice. This article presents results that were obtained on punch biopsies of horse skin, (dental) alveolus of ponies and chondro-osseous samples from the tarsus of foals studied with the new high resolution micro-CT set-up (HRXCT) at the Ghent University (Belgium) (http://www.ugct.ugent.be). This state-of-the-art set-up provides a 1 micron resolution and is therefore ideally suited for a direct comparison with standard light microscopy–based histology.