We compared the gene expression profiles of human dental pulp stem cells (DPSCs) and bone marrow stromal stem cells (BMSSCs) as representative populations of odontoprogenitor and osteoprogenitor cells, respectively. Total RNA from primary cultures was reverse-transcribed to generate cDNA probes and then hybridized with the Research Genetics human gene microarray filter GF211. The microarrays were analyzed using the PATHWAYS software package. Human DPSCs and BMSSCs were found to have a similar level of gene expression for more than 4000 known human genes. A few differentially expressed genes, including collagen type XVIII alpha1, insulin-like growth factor-2 (IGF-2), discordin domain tyrosine kinase 2, NAD(P)H menadione oxidoreductase, homolog 2 of Drosophila large disk, and cyclin-dependent kinase 6 were highly expressed in DPSCs, whereas insulin-like growth factor binding protein-7 (IGFBP-7), and collagen type I alpha2 were more highly expressed in BMSSCs. Furthermore, we confirmed the differential expression of these genes by semiquantitative polymerase chain reaction (PCR) and northern blot hybridization. The protein expression patterns for both IGF-2 and IGFBP-7 correlated with the differential mRNA levels seen between DPSCs and BMSSCs. This report describes the gene expression patterns of two distinct precursor populations associated with mineralized tissue, and provides a basis for further characterization of the functional roles for many of these genes in the development of dentin and bone.