Phase-change memory is a promising candidate for the next generation of non-volatile memory devices. This technology utilizes reversible phase transitions between amorphous and crystalline phases of a recording material, and has been successfully used in rewritable optical data storage, revealing its feasibility. In spite of the importance of understanding the nucleation and growth processes that play a critical role in the phase transition, this understanding is still incomplete. Here, we present observations of the early stages of crystallization in Ge2Sb2Te5 materials through ab initio molecular-dynamics simulations. Planar structures, including fourfold rings and planes, play an important role in the formation and growth of crystalline clusters in the amorphous matrix. At the same time, vacancies facilitate crystallization by providing space at the glass–crystalline interface for atomic diffusion, which results in fast crystal growth, as observed in simulations and experiments. The microscopic mechanism of crystallization presented here may deepen our understanding of the phase transition occurring in real devices, providing an opportunity to optimize the memory performance of phase-change materials.