The periodontium is the set of tissues responsible for tooth anchorage, and consists of interconnected layers of mineralized and unmineralized tissues (bone, ligament and cementum). The ligament-cementum interface is a particularly elegant example of biological control of mineralization and the controlling factors are poorly understood. Here we use a tissue-based in vitro model of mineralization, in which sections of demineralized mouse jaw remineralize with the same selectivity as found in vivo, to probe the molecular mechanism of control over collagen mineralization in the periodontium. Removal or enzymatic cleavage of noncollagenous proteins-have very similar effects: a reduction in the rate of remineralization that is much more drastic in cementum than in dentin. The periodontal ligament does not mineralize within experimental parameters even after protein removal/digestion. Dephosphorylation results in a slight reduction in mineralization in dentin and cementum. Understanding the mechanisms controlling selective mineralization in the periodontium will help elucidate the molecular factors controlling collagen biomienralization, and provide inspiration for the development of scaffolds for regeneration of hard soft tissue interfaces.