We have synthesized epitaxially-grown iron disilicide (FeSi2) nanoparticles using an electron-beam evaporation technique and characterized them by transmission electron microscopy (TEM). An Fe film was deposited on a Si(100) substrate, followed by thermal annealing at 1073 K for 2 h. It was found that epitaxially-grown nanoparticles with an average size of ~10 nm were formed just beneath the Si surface, suggesting that the deposited Fe atoms diffuse into the substrate. Every single phase of nanoparticles was examined in detail by high-resolution TEM observation, nano-beam electron diffraction, and energy-dispersive x-ray spectroscopy. Plane-view and cross-sectional TEM observations revealed that these nanoparticles consist of α-, β-, and γ-FeSi2. It was found that the morphology of nanoparticles is closely related to the phases. The α- and β- phases consist of angled hemisphere and asymmetric triangle-shaped nanoparticles, respectively, while γ-phase is hemispherical or columnar-shaped nanoparticles. These particle morphologies are discussed with respect to the lattice mismatches between the particles and the matrix.