Sub-100-nm silicon nanohole arrays were fabricated by a combination of the site-selective electroless deposition of noble metals through anodic porous alumina and the subsequent metal-assisted chemical etching. Under optimum conditions, the formation of deep straight holes with an ordered periodicity (e.g., 100 nm interval, 40 nm diameter, and high aspect ratio of 50) was successfully achieved. By using the present method, the fabrication of silicon nanohole arrays with 60-nm periodicity was also achieved.