Molecular methods are emerging as important tools for diagnosis and therapy of patients with leukemia. First, the development of conventional Southern blot analysis has facilitated the detection of rearrangements in immunoglobulin and T-cell receptor genes. Moreover, many chimeric genes involved in balanced translocation have identified significant classifications of leukemia patients by cytogenetic techniques such fluorescent in situ hybridization (FISH) and reverse-transcriptase polymerase chain reaction (RT-PCR). These techniques provide an advantage in monitoring minimal residual disease (MRD). Furthermore, recent gene expression analysis with quantitative PCR assays such as real-time PCR have developed the early diagnosis and monitoring of MRD. These molecular-based diagnoses have contributed to the clinical decision-making process in the diagnosis of leukemia.