In this study, we examined the role of the enamel matrix protein, ameloblastin, in bone growth and remodelling, and attempted to identify some of the molecular mechanisms involved in these processes. The effects of recombinant ameloblastin (rAmbn) were tested in vivo in rats, and in vitro in primary human mesenchymal stem cells, osteoblasts, chondrocytes, and osteoclasts. We used a microarray technique to identify genes that were regulated in human osteoblasts and verified our findings using multiplex protein analysis and real-time RT-PCR. Recombinant ameloblastin was found to stimulate bone healing in vivo, and to enhance the proliferation of mesenchymal stem cells and osteoblasts, as well as the differentiation of osteoclast precursor cells in vitro. The most profound effect was on the regulation of genes related to immune responses as well as on the expression of cytokines and markers of bone cell differentiation, indicating that ameloblastin has an effect on mesenchymal cell differentiation. A receptor has not yet been identified, but we found rAmbn to induce, directly and indirectly, signal transducer and activator of transcription (STAT) 1 and 2 and downstream factors in the interferon pathway.