This chapter examines some of the available techniques for analyzing a protein interaction network (PIN) when depicted as an undirected graph. Within this graph, algorithms have been developed which identify “notable” smaller building blocks called network motifs. The authors examine these algorithms by dividing them into two broad categories based on two de?nitions of “notable”: (a) statistically-based methods and (b) frequency-based methods. They describe how these two classes of algorithms differ not only in terms of ef?ciency, but also in terms of the type of results that they report. Some publicly-available programs are demonstrated as part of their comparison. While most of the techniques are generic and were originally proposed for other types of networks, the focus of this chapter is on the application of these methods and software tools to PINs.