Cx3cl1, also called fractalkine, is located at 19p12, and encodes the chemokine (C-X3-C motif) ligand 1 protein. This protein contains 393 amino acids, and is the only member of the chemokine CX3C subfamily. CX3CR1 is the specific receptor of Cx3cl1, and the binding of this ligand and its receptor participates in a variety of physiological and pathological processes. Through employing microarray technology we demonstrated for the first time that Cx3cl1 was upregulated in osteogenic-induced rat bone marrow mesenchymal stem cells (BMSCs). To analyze the gene expression profiling of Cx3cl1 in osteogenic-induced rat BMSCs at different times, real-time quantitative polymerase chain reaction (real-time PCR) was used to assay Cx3cl1 mRNA. The results showed that the expression of Cx3cl1 in osteogenic-induced rat BMSCs increased consistently for 28 days with a peak at day 21, and Cx3cl1 may be correlated with osteogenic differentiation of BMSCs. Based on bioinformatic analyses, we hypothesize that Cx3cl1 may be beneficial to the formation of the osteoplastic microenvironment by regulating cellular distribution and aggregation, and by promoting cellular mutual induction and paracrine. Cx3cl1 may also be involved in osteogenic differentiation and bone formation of BMSCs through an increase in Runx2 transcription by activating p38 mitogen-activated protein kinase (MAPK).