Under near-physiological pH, temperature, and ionic strength, amelogenin (Amel) accelerates hydroxyapatite (HAP) nucleation kinetics, decreasing the induction time in a concentration-dependent manner. Hierarchically organized apatite microstructures are achieved by self-assembly involving nucleated nanocrystallites and Amel oligomers and nanospheres at low supersaturations and protein concentrations in a slow and well-controlled constant composition (CC) system. The CC method allows the capture of an intermediate structure, the nanorod, following the formation of the critical nuclei at the earliest nucleation stages of calcium phosphate crystallization. The nanorod building blocks form spontaneously by synergistic interactions between flexible Amel protein assemblies and rigid calcium phosphate nanocrystallites. These intermediate structures further assemble by a self-epitaxial growth mechanism to form the final hierarchically organized microstructures that are compositionally and morphologically similar to natural enamel. This in vitro observation provides direct evidence that Amel promotes apatite crystallization and organization. We interpret our observations to propose that in vivo Amel may maximally exert an influence on the structural control of developing enamel crystals at the earliest nucleation stages.