The active form of vitamin D (1, Alpha 25-Hydroxyvitamin D3; [1α,25(OH)2D3]) is associated with multiple cellular processes, including bone formation. Severe vitamin D deficiency (as defined by serum 25-Hydroxyvitamin D <30nmol/L) typically results in growth retardation, rickets and osteomalacia. Conversely, 1α,25-(OH)2D3 treatment demonstrates anabolic effects on bone, which could be explained via its action on differentiating mesenchymal stem cells (MSCs). This study investigated the effect of 1α,25-(OH)2D3 on osteogenic and adipogenic differentiation of human MSCs (hMSC). We examined 12,000 human genes and expressed sequence tags on the array Human Genome U95A via Affymetrix DNA array. We confirmed genes with higher and lower expression by reverse transcription-polymerase chain reaction. We found that differentiating hMSC treated with 1α,25-(OH)2D3 exhibited a significantly higher expression of distinct osteogenic genes (CYP24A1, DSP, FBLN2, HYAL3, MN1 and TBCD) and adipogenic genes (Fibulin 2 [FBLN2], DSP and G0S2) when compared to undifferentiating hMSCs. In addition, FBLN2 showed a significantly higher expression when treated with 1α,25-(OH)2D3 in both adipogenic and osteogenic conditions. Meanwhile, CYP24A1, which is associated with 1α,25-(OH)2D3 degradation, had reduced expression in adipogenic compared to osteogenic and MSCs growth media. In summary, our gene array analysis identified a direct effect of 1α,25-(OH)2D3 on a set of genes required for hMSCs differentiation, thus improving our understanding of the effect of the active form on vitamin D on bone metabolism.