We established a quantitative real-time RT-PCR assay for the detection of chimeric BCR-ABL transcripts in archival formalin-fixed bone marrow trephines, both acrylate-embedded and paraffin-embedded. This new methodology enables determination of transcript levels in direct comparison to histopathological findings and therapeutic interventions during the time course of the disease in a retrospective and a prospective manner. We found an excellent correlation between the quantitative molecular data and the morphological evaluation as well as the clinical outcome for a cohort of chronic myeloid leukemia patients (n = 10). To the best of our knowledge, this is the first study demonstrating the feasibility of large-scale quantitative expression analysis in archival bone marrow trephines for monitoring molecular markers over several years or even decades.