Co-immunoprecipitation (co-IP) is a prominent technique for evaluating protein-protein interactions. Currently, large quantities of protein are required to perform co-IP followed by mass spectrometric or Western blot analyses of the interacting proteins. Here catenin-cadherin complexes were employed to establish a multiplexed microsphere-based co-immunoprecipitation (micro co-IP) protocol that allows the analysis of different complexes of a given protein with various interacting proteins within a single experiment using a limited amount of sample material.