Si (001) wafers were implanted at room temperature with 50-keV Fe ions to different doses and subsequently crystallized either by rapid thermal annealing (RTA) (900°C, 120 s) or by Si+ irradiation (500 keV, 320 °C). Transmission electron microscopy, as well as Rutherford backscattering and channeling, were used to study the phase formation of FeSi2 in Si. Depending on the implantation dose and the crystallization process, three phases of FeSi2 were produced. While RTA results in the formation of β-FeSi2, ion irradiation promotes the growth of either cubic FeSi2 phase for low implantation doses (< = 4 at.% Fe) or a-FeSi2 for high implantation doses (≈18 at.% Fe). All these phases of FeSi2 were found to grow epitaxially in the Si matrix and their orientation relationships relative to Si have been determined. The interfacial energy between FeSi2 and Si appears to be an important factor in determining the final structure of FeSi2.