The study was purpose to evaluate the value of real time quantitative-PCR for monitoring IgH level in patients with B-cell malignancy after hematopoietic stem cell transplantation (HSCT). Quantification of IgH levels was performed on bone marrow mononuclear cells from 9 patients with B-cell malignancy before and after HSCT by PCR using the consensus JH TaqMan probe in combination with an allele-specific oligonucleotide (ASO) upstream primer. The IgH levels was normalized by control gene GAPDH. The results indicated that the reproducible sensitivity of RQ-PCR was 1 copy, the significant reduction of IgH copies was observed in bone marrow samples of 9 patients at one month post HSCT (6.67x10(3)/10(6) GAPDH vs 29/10(6) GAPDH, p<0.01). 3 out of 9 patients who achieved complete clinical and molecular cytogenetic remission (CCyR) contained persistently measurable low IgH level of 10(2)/10(6) GAPDH within 15 months and no detectable IgH at 18 months post HSCT. Whereas 5 out of 9 patients whose IgH copies were less than 10(2)/10(6) GAPDH within 3 months and less than 10(3)/10(6) GAPDH 3 months post HSCT achieved a sustained complete remission (CR). IgH copies in one patient were 4.5x10(3)/10(6) GAPDH at 3 months post HSCT, who relapsed at 4 months post HSCT. The median levels of tumor contamination in the stem cell harvests from 8 patients measured by RQ PCR were 3.68x10(2) (0-1720)/10(6) GAPDH. RQ PCR showed that PBPC harvests were less contaminated than BM harvests [75 (0-890)/10(6) GAPDH vs 1.1x10(3) (527-1720)/10(6) GAPDH, p<0.05]. 8 patients whose stem cell harvest were avaiable for RQ PCR were still in CR despite of the tumor contamination. The level of tumor contamination in stem cell harvest well correlated with IgH levels at diagnosis and one month after HSCT (r=0.810, r=0.708, p<0.05). It is concluded that RQ PCR can effectively monitor the IgH levels in patients with B-cell malignancy after auto-HSCT. 10(3)/10(6) GAPDH within 3 months post HSCT may be a cut-off level of IgH copies, which may be used to evaluate different prognoses of patients.