The steroid hormone 1,25-dihydroxyvitamin D3 (1,25(OH) 2 D 3 ) inhibits osteogenesis while stimulating adipogenesis in vitro. We hypothesized that 1,25(OH) 2 D 3 redirects the fate of osteoblast/adipocyte bipotential progenitors and other potential progenitors towards adipogenesis, a process possibly underlying the pathogenesis of osteopenic diseases such as osteoporosis. We therefore tested the global effects of 1,25(OH) 2 D 3 on the recruitment of mesenchymal progenitors including osteogenic, chondrogenic, adipogenic and myogenic lineages (colony forming cell (CFC)-osteoblast (CFC-O), CFC-chondrocyte (CFC-C), CFC-adipocyte (CFC-A), and CFC-myoblast (CFC-M) respectively) in rat calvaria (RC) cell populations using gene expression profiling of single cell-derived colonies. Based on expression of lineage specific transcripts, 86% of single cell-derived colonies in untreated cultures simultaneously co-expressed transcripts of two, three, or four of the mesenchymal lineages tested. The distribution of mesenchymal progenitors in 1,25(OH) 2 D 3 -treated cultures was significantly changed compared with the control group, i.e. CFC-O were reduced (from 6 to 0%) and CFC-O/A bipotential (0 to 8·2%), CFC-C (4 to 10·2%) and CFC-Fibroblast (CFC-F) (4 to 16%) were increased. 1,25(OH) 2 D 3 did not affect the frequency of tri-or tetra-lineage colonies. Single lineage CFC-A colonies were not detected in either the control or 1,25(OH) 2 D 3 treatment group under the conditions tested. Since the parietal bones used for cell isolation derive from neuroectoderm, we also analyzed for expression of the neural markers nestin and 3 tubulin in these colonies. Surprisingly, 90% (45 of 50) of the colonies in the control group expressed neural markers, a frequency not changed by 1,25(OH) 2 D 3 treatment. The current studies demonstrate the global and developmental stage-specific effects of 1,25(OH) 2 D 3 on mesenchymal lineage progenitors, and suggest that the effects of 1,25(OH) 2 D 3 on osteogenesis and adipogenesis in RC populations are mediated, at least in part, by increased recruitment of CFC-O/A, but not CFC-A type precursors.