Sea urchin embryos form their calcitic spicular skeletons via a transient precursor phase composed of amorphous calcium carbonate (ACC). Transition of ACC to calcite in whole larvae and isolated spicules during development has been monitored using X-ray absorption spectroscopy (XAS). Remarkably, the changing nature of the mineral phase can clearly be monitored in the whole embryo samples. More detailed analyses of isolated spicules at different stages of development using both XAS and infrared spectroscopy demonstrate that the short-range order of the transient ACC phase resembles calcite, even though infrared spectra show that the spicules are mostly composed of an amorphous mineral phase. The coordination sphere is at first distorted but soon adopts the octahedral symmetry typical of calcite. Long-range lattice rearrangement follows to form the calcite single crystal of the mature spicule. These studies demonstrate the feasibility of real-time monitoring of mineralized-tissue development using XAS, including the structural characterization of transient amorphous phases at the atomic level.