This paper presents pathological changes indicative of type II Klippel–Feil syndrome identified in the skeleton of a child uncovered in one of the oldest Christian churches in Poland (first half of the 11th century) with the archaeological layer containing the burial dated to the 13th–15th centuries. The age at death of the child was estimated at 9 to 10 years. The third and fourth cervical vertebrae of this individual were fused asymmetrically, leading to torticollis. The apex of the dens axis (odontoid process) was V‐shaped, which is consistent with clinical descriptions of ossiculum terminale. The laminae of the second sacral vertebra were found to be fused but positioned asymmetrically with respect to one another, while the laminae of the third and fourth vertebrae were hypoplastic, suggesting spina bifida of the sacrum. This configuration of anomalies is symptomatic of type II Klippel–Feil syndrome. In addition, the studied individual revealed heterotopic ossification on the supinator crest of the ulna, which may have arisen as a result of dislocation of the elbow joint. Copyright © 2017 John Wiley & Sons, Ltd.