New treatments that may change the course of a disease or have potential carcinogenicity can result in the emergence of new cytogenetic or clinical disorders. We report here the cytogenetic evolution of 52 cases of Philadelphia (Ph)-positive myelogenous leukemia (CML) receiving interferon-alpha (IFN-alpha) therapy compared with that of 59 Ph-positive CML cases treated with busulfan (BU) or hydroxyurea (HY). Twenty-one percent of the CML patients receiving IFN-alpha displayed unusual secondary abnormalities, among which alteration of the long arm of chromosome 3, del(7), and del(9) were recurrent. The frequency of these unusual secondary changes was significantly higher than in CML cases after Bu or Hy treatment (P = 0.02). Three of the 11 IFN-alpha-treated CML patients displayed cytogenetic evolution in the chronic phase and, in two cases, the cytogenetic findings were transient, inasmuch as they disappeared upon withdrawal of IFN-alpha. In addition, a majority of cytogenetic abnormalities involved chromosome 3 at bands 3q21 and 3q26, which corresponds to the locus of EVI1, a gene implicated in the development or progression of human myeloid leukemias. Possible explanations include: toxicity of IFN-alpha by effect on bone marrow stroma, immune-modulating effects of IFN-alpha, and mutagenic effects of IFN-alpha. The mechanisms underlying these cytogenetic changes remain to be elucidated. However, our data suggest that IFN-alpha induces additional cytogenetic abnormalities even in the chronic phase through its immune-modulating effects and that these unusual cytogenetic abnormalities do not alter the history of CML.