Many chromosomal translocations involved in leukemia have been defined at the molecular level in recent years. In addition to advancing the understanding of pathological mechanisms underlying the transformation process, the cloning and sequencing of the genes altered by the translocations have provided new tools for diagnosis and monitoring of patients. In particular, the polymerase chain reaction (PCR) method yields sensitive and accurate diagnostic and prognostic information. Minimal residual disease (MRD) is not clearly defined. In ALL we define MRD as fewer than 5% blast cells in the bone marrow by conventional cytology and proof of leukemic cells with more sensitive methods. The techniques for detecting MRD are imaging for detection of single leukemic cells in the blood, bone marrow, or other tissues by means of immunocytology or PCR/RT-PCR. Highly sensitive PCR, immunocytology, FACS analysis, or conventional cytology are important tools to use in the process of deciding on appropriate therapy. Detection limits at present are 10(-2) for cytology and FISH, up to 10(-4) for immunological procedures, and 10(-5) to 10(-6) for PCR. But multiple methods also imply the possibility of mistakes (e.g., PCR). The question must be raised what method should be decisive in assessing MRD for evaluating autologous peripheral blood stem cells (PBSC) or autologous bone marrow transplants? Prospective studies will have to answer the question whether MRD should be treated or not and whether purging of bone marrow or PBSC is useful or damaging. When applied, should a positive or a negative immunopurging or a chemotherapeutic purging be used? MRD refers to the organism of the patient as well as to the peripheral blood stem cells and autologous bone marrow that had been taken before myeloablative therapy and kept for retransfusion.