Post-translational modification by the small ubiquitin-like modifier (SUMO) family of proteins is an important cellular regulatory mechanism, and in recent years has been found to be involved in a large and diverse set of signaling pathways. Most of these SUMO-dependent functions appear to be mediated by the interaction between SUMO attached to the modified proteins and a “SUMO-binding motif” (SBM or SIM) on receptor proteins. Nuclear magnetic resonance (NMR) studies were instrumental in the identification of this SUMO-binding motif, and reveal that, depending on the sequence context, this motif can bind to SUMO in two opposing orientations. In this paper, we provide an overview of how NMR methods can be used to identify such short conserved binding motifs and structurally characterize their interaction with target proteins. These experiments are complementary to traditional biochemical methods and are applicable to the identification of other SUMO-binding motifs and to the studies of other ubiquitin-like modification systems.