Membrane proteins fulfill a variety of important cellular functions such as transport, signal transduction and energy conversion. They often appear as part of larger protein complexes or bind transiently to interaction partners. The detailed analysis of protein-protein interactions leads to a better understanding of the function of the proteins and their mode of action. The yeast split-ubiquitin system provides an easy-to-use technique to analyze the interactions between membrane proteins, and it has been applied to a large variety of proteins from different membranes and organisms. In this report, we describe the principle of the yeast split-ubiquitin system and provide step-by-step instructions to analyze the pairwise interaction between two membrane proteins or between a membrane protein and its soluble interaction partner.