Chronic myeloid leukemia (CML) is a stem-cell disease characterized by multilineage expansion of clonal BCR/ABL+ cells. Transformation from chronic into accelerated and blast phase of CML is usually associated with drug resistance and is accompanied by typical clinical and/or laboratory features, such as splenomegaly, increase in precursor cells, disturbed megakaryopoiesis, basophilia or marrow fibrosis. Because of new treatment options, early recognition of disease-acceleration is of importance. In this article, we review most recent developments in diagnostic procedures employing basophil-related biochemical and histopathological markers. These tests are useful to quantitate basophil-lineage cells in the peripheral blood in CML, to determine and quantify basophilia in the bone marrow, and to detect focal accumulations of blast cells and megakaryocytes as well as increased angiogenesis and fibrosis in bone marrow sections. Application of these markers may assist in determining the phase of disease and may help to better predict the prognosis in individual patients.