In a previous work, based on an in vitro entire tooth culture model of human immature third molars, we demonstrated that perivascular progenitor cells can proliferate and migrate to the injury site after pulp exposure. In this work, we investigated the differentiation of cells after direct capping with biomaterials classically used in restorative dentistry. Histological staining after direct pulp capping with Calcium Hydroxide XR 1 or MTA revealed early and progressive mineralized foci formation containing BrdU-labeled sequestered cells. The molecular characterization of the matrix and the sequestered cells by immunohistochemistry (Collagene type I, Dentin sialoprotein, and Nestin) clearly demonstrates that these areas share common characteristics of the mineralized matrix of reparative dentin formed by odontoblast-like cells. This reproduces some features of the pulp responses after applying these materials in vivo and demonstrates that the entire tooth culture model reproduces a part of the early steps of dentin regeneration in vivo. Its future development may be useful in studying the effects of biomaterials on this process.