Tissue engineering applications aim to replace or regenerate damaged tissues through a combination of cells, three-dimensional scaffolds, and signaling molecules [1]. The endochondral approach to bone tissue engineering [2], which involves remodeling of an intermittent hypertrophic cartilaginous template, may be superior to the traditional intramembranous approach. Naturally derived hydrogels have been used extensively in tissue engineering applications [3]. Mesenchymal stem cell (MSC) seeded hydrogels may be a particularly powerful tool in scaling-up engineered endochondral bone grafts as the low oxygen conditions that develop within large constructs enhance in vitro chondrogenic differentiation and functional development [4]. A key requirement however, is that the hydrogel must allow for remodeling of the engineered hypertrophic cartilage into bone and also facilitate vascularization of the graft. The first objective of this study was to compare the capacity of different naturally derived hydrogels (alginate, chitosan, and fibrin) to generate in vivo endochondral bone. The secondary objective was to investigate the possibility of engineering a ‘scaled-up’ anatomically accurate distal phalange as a paradigm for whole bone tissue engineering.