Two types of periodic nanostructures, self-organized nanodots and nanolines, were fabricated on the surfaces of indium-tin-oxide (ITO) films using femtosecond laser pulse irradiation. Multiple periodicities (approximately 800 nm and 400 nm) were clearly observed on the ITO films with nanodot and nanoline structures and were identified using two-dimensional Fourier transformation patterns. Both nanostructures show the anisotropic transmission characteristics in the visible range, which are strongly correlated with the geometry and the metallic content of the laser-induced nanostructures.