We report a 63-year-old woman with myelodysplastic syndrome (MDS), refractory anaemia with ring sideroblasts (RARS), and blood basophilia with pathological forms. Karyotype analysis revealed a complex rearrangement: 46,XX,del(3)(p13p25),del(5)(q13q33),der(16)t(1;16) (p13;q12)/47,idem,add(20)(?p11)/49,idem, + add(1)(q32),add(20)(?p11), + mar/46,XX. Karyotype, immunophenotype and in situ hybridization studies by the MAC (morphology antibody chromosomes) combination technique revealed the chromosomal abnormality in granulocytic/monocytic and erythrocytic metaphase cells. Also mature basophils and other granulocytes were involved with the abnormality. We suggest that our patient with the MDS has a stem cell disorder affecting all myeloid cell lineages and that basophilia constitutes a part of the malignant process.