The Microarray Assay for Realtime Coregulator-Nuclear receptor Interaction (MARCoNI) technology allows the identification of nuclear receptor-coregulator interactions via flow-through microarrays. As such, differences in the coregulator profile between distinct nuclear receptors or of a single receptor in agonist or antagonist mode can be investigated, even in a single run. In this chapter, the method how to perform these peptide microarrays with cell lysates containing the overexpressed glucocorticoid receptor is described, as well as the influence of assay parameters, variations to the protocol, and data analysis.