Nanoscale patterns are created on silicon (100) surfaces via cathodic electrografting of alkyls. Self-assembled polystyrene microspheres on silicon surfaces can serve as dielectric masks. Cathodic potentials are applied to masked substrates in liquid hexynoic acid or phenylacetylene leading to the formation of nanoscale islands with monolayers of covalently bound functional groups on silicon. Silicon surfaces functionalized with islands of hexynoic acid are demonstrated using a biotin reaction. Cyclic voltammetry, scanning electron microscopy, and atomic force microscopy are used to characterize the patterned surfaces. The method provides a facile and high throughput process for spatially defining the local reactions on silicon with nanometer-scale resolution. (C) 2009 The Electrochemical Society. [DOI: 10.1149/1.3121243] All rights reserved.