Disease recurrence is a major problem in patients receiving bone marrow transplantation for chronic myeloid leukemia. Residual malignant cells are the most likely source of recurrence. Detection of minimal residual disease early during therapy may provide an additional prognostic value and help in identifying patients who are at high risk of relapse. PCR followed by hybridization is the most sensitive method to investigate the persistence of leukemic cells. However, more reproducible methods suitable to standardization and quantification are required in clinical practice. In this study, we describe a novel PCR assay combined with immunological and colorimetric detection of the bcr-rearrangement. Residual bcr/abl rearranged cells were observed in 7 patients. Our results show that the assay is equally sensitive as RT-PCR, more versatile in terms of standardization and easily adaptable as a diagnostic test.