Pluripotent cells, such as embryonic stem cells (ESCs), divide indefinitely and can differentiate to form mineralised nodules in response to osteogenic supplements. This suggests that they may be used as a cell source for bone replacement strategies. Here, we related the expression of osteogenic and chondrogenic genes in cultures of murine ESCs, marrow stromal cells (MSCs) and calvarial osteoblasts (OBs) cultured under osteogenic conditions to the biochemical composition and quantity of mineral formed. Mineralisation, measured by calcium sequestration, was >2-fold greater in ESC cultures than in either MSCs or OBs. Micro-Raman spectroscopy and spectral mapping revealed a lower mineral-to-matrix ratio and confirmed a more diffuse pattern of mineralisation in ESCs compared to MSCs and OBs. Baseline expression of chondrogenic and osteogenic genes was between 1 and 4 orders of magnitude greater in MSCs and OBs than in ESCs. Osteogenic culture of MSCs and OBs was accompanied by increases in osteogenic gene expression by factors of ~100 compared to only ~10 in ESCs. Consequentially, peak expression of osteogenic and chondrogenic genes was greater in MSCs and OBs than ESCs by factors of 100-1000, despite the fact that mineralisation was more extensive in ESCs than either MSCs or OBs. We also observed significant cell death in ESC nodules. We conclude that the mineralised material observed in cultures of murine ESCs during osteogenic differentiation may accumulate non-specifically, perhaps in necrotic cell layers, and that thorough characterisation of the tissue formed by ESCs must be achieved before these cells can be considered as a cell source for clinical applications.