Although much is known about the hormonal regulation of hard tissue development, much less is known about the nuclear regulatory molecules that affect the process. Homeobox-containing genes are thought to encode DNA-binding transcriptional factors which control the expression of other genes. In this study, molecular cloning of Msx homeobox-containing genes from a bovine odontoblast library and a human dental pulp-derived cells library was performed, and also the expression of mRNAs for Hox and Msx homeobox-containing genes during ectopic bone formation induced by BMP was investigated. Screening of a bovine odontoblast cDNA library and a human dental pulp-derived cells library with murine Msx-1 and Msx-2 cDNA probes led to the isolation of several positive clones. All of the clones from a bovine odontoblast library encoded the bovine counterpart for human MSX-1. All of the clones from a human dental pulp-derived cells library encoded the human counterpart for murine Msx-2. Northern blot analysis probed with a human MSX-2 cDNA indicated the expression of 2.2kb and 1.2kb mRNA in human dental pulp-derived cells. Polymerase chain reaction (PCR)-based analysis in the BMP-implanted tissue revealed that nine rat homologues of Hox homeobox-containing genes were expressed in the early cell migration stage and that two Msx genes were expressed in the cartilage and bone differentiation stages. The PCR study provided evidence of dynamic changes in the BMP-induced homeobox gene expression.