Background European hedgehogs (Erinaceus europaeus) are small insectivorous mammals common in Europe. With increased urbanization, the species become more frequent in the cities and near other human dwellings. The anatomy of the species with the use of diagnostic imaging techniques along with the classical anatomical methodology has not been researched before. In addition to the description of this species' skull, the data may contribute to progress in hedgehog medicine, delivering a basis for diagnosing and treating head trauma in this species. Results Cadavers of 30 European hedgehogs have been used to study the anatomy of the head of the species. Along with classical anatomical techniques – latex and corrosion cast specimens, x-ray, and cone-bean computed tomography scans were performed. The methods were then compared, and the detailed anatomy of the head was described. The skull of the Western European hedgehog was elongated and oval in shape, and could be divided into two distinct regions: one formed of neurocranial bones and the other of facial bones. The neurocranium was composed of the following bones: the occipital, interparietal, parietal, frontal, temporal, sphenoid, ethmoid, and pterygoid bones. The following facial bones were identified: the incisive, nasal, maxilla, zygomatic, palatine, vomer, and the mandible. The most important findings include the primitive tympanic bullae, the absence of a supraorbital foramen, and the lacrimal bones, which were indistinguishably fused with the maxillae. Conclusions The results of the study may be used in future research on the comparative anatomy of the other members of the Eulipotyphla order. With the increase of hedgehogs in the cities, it is important to establish new diagnostic and treatment protocols for wildlife rehabilitation centers. Anatomical and radiological descriptions may be used as a base for such work. The anatomical features of the hedgehog skull described in the study may prove useful for further studies from a comparative anatomical perspective. Additionally, the data may serve as a basis for developing identification guidelines for archaeological studies and forensic research.