In this study, we established an in vitro model of osteogenic-inductive differentiation of rat bone marrow mesenchymal stem cells (BMSCs) to determine the mechanisms and relative gene function underlying BMSCs osteogenesis. Osteoplastic differentiation of the third generation BMSCs was induced with the alpha-minimal essential medium containing beta-glyceraldehyde-3-phosphate, L: -ascorbic acid, dexamethasone and 1,25-2(OH)2 vitamin D3 prior to applying gene chip technology (also called microarray technology) for global gene expression screening. Real-time quantitative PCR (Real-time PCR) was used to determine the temporal profile of mRNA expression of regulated genes during osteogenic differentiation of BMSCs. A bioinformatic analysis was utilized to determine the functional significance of the identified osteogenic-related genes. Purkinje cell protein 4 (Pcp4) mRNA expression was identified by the gene chip screening as being up-regulated during osteoplastic differentiation of BMSCs. Real-time PCR analysis confirmed the increased expression of Pcp4 mRNA expression during osteoplastic differentiation of BMSCs with an upward trend that peaked at day 14. The bioinformatic analysis identified Pcp4 as a gene involved in the deposition of calcium and the modulation of CaM-dependent protein kinase. Thus, we hypothesize that Pcp4 osteoplastic differentiation of BMSCs is mediated in part via Pcp4-induced calcium deposition to form mineral nodules and modulation of certain signal transduction pathways of BMPs.