Scanning tunneling microscopy and density functional theory calculations were used to study the structure of the Au(100) surface after ion bombardment. The results indicate a development of two phases: the quasi-hexagonal (hex) and the (1 × 1) on the surface. A decrease in the number of surface atoms caused by ion bombardment leads to the development of a coexistence of phases inside the surface layer. Our experimental data and theoretical results rule out a scenario that the unreconstructed (1 × 1) domains under study represent a subsurface atomic layer revealed by ion sputtering. The hex phase is anisotropic, with the quantized width in accord with (6n + 1) formula. In certain conditions, nanowire-like structures consisting of seven atomic rows of alternating height are developed on the surface.