Clonal IgH gene rearrangement as a gene marker of B-cell malignancies, a new method of polymerase chain reaction amplification in conjunction with single-strand conformational polymorphism (PCR-SSCP) analysis was performed on the stored bone marrow slide specimens from patients with B cell neoplasm for detecting minimal residual disease (MRD). The method was sensitive to 1-2 malignant B-cells in 1,000 normal bone marrow cells. In untreated patients with B-NHL, the incidence of MRD in bone marrow specimens was 68.4% (26/38). Patients with MRD in bone marrow had a shorter survival time than those without (P < 0.05). In patients with B-ALL in complete clinical remission, the incidence of MRD in bone marrow was 71.4% (15/21). There was a tendency of relapse in patients with MRD in bone marrow but persistent complete remission in patients without. The results showed that detection of MRD in bone marrow may provide some important information for assessing prognosis and predicting relapse in patients with B-cell malignancy.