With recent development and progress achieved in the diagnosis and treatment of leukemia, relapse of disease still remains as the major problem in clinical management and the minimal residual disease (MRD) has been confirmed to be associated with leukemia relapse in the past decades. Due to the low sensitivity, morphology-based assays have limitation in the MRD monitoring. With the development of molecular assays, especially the real-time RT-PCR method have been a sensitive, precise and reliable tool to MRD detection. Numerous clinical studies demonstrated that the existence of MRD reflects the clinical and molecular response, and remain as a major prognostic factor for leukemia. Another important application of MRD detection is to evaluate the efficacy of different therapy at molecular level. In this paper, the different methods and their clinical application for MRD detection were systemically reviewed and it is confident that the establishment of standardized MRD detection system will be important in the clinical prevention for relapse of leukemia.