Key Clinical Message Cleidocranial dysplasia (CCD) is a rare genetic skeletal disorder with only few cases reported in Africa, mostly based on clinical and radiological findings. We report the first case in Mali, caused by a novel de novo variant in the RUNX2 gene. Cleidocranial dysplasia (CCD) is a rare autosomal dominant skeletal dysplasia characterized by an aplastic/hypoplastic clavicles, patent sutures and fontanels, dental abnormalities and a variety of other skeletal changes. We report a novel de novo variant in the RUNX2 gene causing a severe phenotype of CCD in a Malian girl. Radiological features of cleidocranial dysplasia. (A) The orthopantomogram at age 8 showing germ retention and polyodontia with supernumerary teeth; (B) Chest X‐rays showing a total absence of the clavicles and (C) Pelvic x‐rays showing a left coxa Vara lesion; Brain CT‐scan showing (D) a dilatation of the occipital horns of the lateral ventricles at the time of diagnosis and (E) 3 years later; 3D reconstruction of the CT‐scan of the skull in (F) anterior view showing patent anterior fontanel, the absence of the upper part of the frontal and the parietal bones, (G) posterior view showing the absence of the parietal bone with preservation of the occipital bone, and (H, I) progression of the cranial bone development after 3 years of evolution with a notable reduction of the bone defect.