In patients with dermatomyositis with anti-Mi2 autoantibodies, autoantibodies can enter muscle cells, leading to the aberrant expression of genes normally repressed by the Mi2/nucleosome remodelling and deacetylation (NuRD) complex. However, the mechanism by which autoantibodies interfere with Mi2/NuRD function remains unclear. This study aimed to identify additional autoantibodies in anti-Mi2-positive patients and the epitopes recognised by these autoantibodies.Phage immunoprecipitation sequencing (PhIP-Seq) was used to screen sera from patients with anti-Mi2 autoantibody-positive myositis. Enzyme-linked immunosorbent assays (ELISAs) and luciferase immunoprecipitation system (LIPS) immunoassays were used to detect autoantibodies in sera from healthy controls, patients with myositis, and those with other autoimmune diseases.PhIP-Seq identified autoantibodies recognising the autoimmune regulator (AIRE) in sera from anti-Mi2 autoantibody-positive patients. Both anti-AIRE and anti-Mi2 autoantibodies predominantly recognised a homologous region containing the plant homeodomain zinc finger type I (PHD1), which is critical for AIRE and Mi2/NuRD function. ELISA and LIPS showed that anti-Mi2 autoantibody-positive patients were positive for anti-AIRE autoantibodies, whereas AIRE reactivity was largely absent in healthy comparators, anti-Mi2 autoantibody-negative myositis, and other autoimmune diseases. Affinity-purified anti-Mi2 autoantibodies recognised both Mi2 and AIRE by ELISA, whereas anti-Mi2-depleted fractions did not recognise either protein.Autoantibodies targeting Mi2 recognise AIRE at a shared PHD1 epitope - a conserved motif found in numerous transcriptional regulators. These findings support a model in which anti-Mi2 autoantibodies disrupt the Mi2/NuRD complex, and potentially other PHD1-containing proteins, by interfering with chromatin binding, although further studies are needed to directly demonstrate this mechanism in vivo.