We investigated the skull of a juvenile living in Southern Germany between 1400 and 1800 A.D. A remarkable hemifacial microsomia led to further detailed computed tomographic examination especially of the petrous bone revealing a total bony atresia of the external auditory canal as well as distinct anomalies of the middle ear on the same side. The combination of these findings strongly suggests the diagnosis of Goldenhar syndrome. This very heterogeneous syndrome affects primarily aural, ocular, oral and mandibular development, whereby the constellation of anomalies indicate their origin at approximately 30-45 days of gestation, caused by genetic or intrauterine factors. Despite the lack of clinical information and the absence of soft tissue it was possible to perform a differential diagnosis in this palaeopathological case. Thereby, the use of modern modalities of image reconstructions in this computed tomographic clearly enhanced the supposed diagnosis.