Calcium carbonate is one of the most abundant biominerals. Organisms have developed sophisticated controls over its polymorph, morphology and orientation through protein matrices. However, there are many unknowns as to how the matrices affect the crystallization process, in particular, the initial nucleation. A prevailing view is that crystals form via epitaxy from the templates. Alternatively, a crystalline phase could form through a multistep phase transformation, initiated by the formation of an amorphous phase. Since the amorphous phase is more soluble than the stable crystalline phase, it should be the first solid phase formed during the crystallization and therefore could be prevalent in biomineralization. In fact, amorphous phase minerals have been identified in many organisms and more recent discoveries have suggested that amorphous calcium carbonate is more widespread than commonly supposed in biology, but has been overlooked due to the difficulty of identifying an amorphous phase in the presence of a crystalline phase of the same composition.