AFG3L2 and paraplegin are cognate ATP-dependent metalloproteases that constitute the m-AAA protease complex in the inner mitochondrial membrane. Co-immunoprecipitation (CoIP) is a useful technique for the analysis of protein-protein interaction. Here, we illustrate a protocol to precipitate the complex formed by human epitope-tagged AFG3L2 and paraplegin heterologously expressed in the yeast Saccharomyces cerevisiae. The procedure employs polyclonal anti-AFG3L2 and anti-paraplegin, and monoclonal anti-HA antibodies to investigate the interaction between the two proteins. The protocol can be adapted to the analysis of other protein complexes.