Runt-related transcription factor 2 (RUNX2/Cbfa1) is the main regulatory gene controlling skeletal development and morphogenesis in vertebrates. It is located on chromosome 6p21 and has two functional isoforms (type I and type II) under control of two alternate promoters (P1 and P2). Mutations within RUNX2 are linked to Cleidocranial dysplasia syndrome (CCD) in humans. CCD is an autosomal skeletal disorder characterized by several features such as delayed closure of fontanels, dental abnormalities and hypoplastic clavicles. Here, we summarize recent knowledge about RUNX2 function, mutations and their phenotypic consequences in patients.