Aplastic anemia (AA) is an immune-mediated disorder that overlaps closely with clonal disorders, such as myelodysplastic syndrome and paroxysmal nocturnal hemoglobinuria (PNH). PIGA mutations in PNH clones and functional loss of HLA, including structural HLA mutations, likely represent immune escape clones and correlate with response to immunosuppressive therapy (IST). Somatic mutations typical for myeloid malignancies and age-related clonal hematopoiesis are detected in a proportion of AA patients, but their significance is unclear and seems to depend on whether patients are tested at diagnosis or after IST, patient age and ethnicity, and the methodology of molecular testing used.