Minimal residual disease (MRD) can be easily studied in hematological malignancies by analyses of various fusion transcripts or tumor-specific immunoglobulin heavy-chain or T-cell receptor rearrangements as markers of disease. Correlation between MRD and prognosis has been extensively investigated mostly in acute leukemia and chronic myeloid leukemia. Quantitative aspect seems an essential criterion but the current absence of standardization makes difficult clinical decision according to MRD results. Development of real time quantitative PCR techniques would probably overcome these limitations. Only follicular non-Hodgkin's lymphomas are currently routinely analyzed using BCL2-JH PCR but signification of results obtained in complete remission remains uncertain. Analyses of tumor-specific immunoglobulin heavy-chain or T-cell receptor rearrangements allow physiological study and evaluation of bone marrow purgin system efficacy but are of limited interest in current clinical practice.