Tissue-engineered bone grafts require an osteogenic cell source and a scaffold capable of supporting tissue regeneration. Hydroxyapatite (H), chitosan (C), and gelatin (G), when combined, produce a biomimetic scaffold with a chemical similarity to the main structural components of natural bone tissue. In this study a phase-separation technique was used to produce a porous 3D HCG scaffold, containing a network of cross-linked chitosan and gelatin fibrils coated in hydroxyapatite, with pore size readily controlled by freezing temperature. The HCG scaffolds were then seeded with human mesenchymal stem cells (hMSCs), using a depth filtration system after preconditioning with serum-containing medium for 7 days under either static or perfusion conditions. The effects of static and perfusion media preconditioning on protein adsorption, surface morphology, hMSC attachment, proliferation and osteogenic differentiation were examined. Perfusion preconditioning, as opposed to static preconditioning, enhances adsorption of ECM proteins, which in turn promotes hMSC proliferation and osteogenic differentiation. The results demonstrate the importance of convective flow in modulating the 3D HCG microenvironment and highlight its profound influence on 3D construct development. Copyright © 2011 John Wiley & Sons, Ltd.