Aplastic anemia (AA) is a non-neoplastic hematological disease closely associated with bone marrow failure which is typical of paroxysmal nocturnal hemoglobinuria (PNH) and myelodysplastic syndrome (MDS). The PNH clones can be detected in more than a half of AA patients at onset of the disease, and there is a probability for AA/PNH co-variants to progress to classic hemolytic PNH. At the same time, the AA patients treated by immunosuppressive therapy undergo the risk of disease transformation to MDS and acute myeloid leukemia. Currently known risk factors and possible precursors of such transformation are considered in the brief literature review. In addition to that, the paper provides a case report of AA/PNH transformation to MDS during complete AA remission after immunosuppressive therapy combined with a successful haploidentical transplantation of hematopoietic stem cells.