Self-assembly is an interesting process both for its biological relevance and because it provides a novel approach to complex structures having nanometer-scale dimensions. These structures are difficult or impossible to prepare by traditional methods. In this article, a general review on the use of self-assembled monolayers for chemical patterning is provided. In the first part, functional group transformation of SAMs on flat gold surfaces by chemical reactions is discussed in detail. The use of monolayer-protected gold nanoparticles as model systems for flat gold surfaces is covered with special focus on the transformation of functional groups on the outer SAM layer. Furthermore, techniques that have been used to pattern SAMs are discussed. Among these techniques, microcontact printing and scanning probe lithography are discussed in detail for both their advantages and limitations.