INTRODUCTION: Knowledge of the composition of protein complexes provides key insights into their functions. Immunoaffinity purification provides an effective means for isolating protein complexes and elucidating their composition. Immunoisolation is achieved with antibodies directed either specifically against the proteins of interest or against tags that are coupled to the proteins of interest. This approach uses immunoaffinity purification on magnetic beads coated with antibodies for the rapid and efficient purification of protein complexes from cells or tissues. This protocol describes affinity purification of protein complexes using conjugated magnetic beads.