After having standardized the FCBA method for our laboratory, we demonstrated that i) a minimum number of fresh collected cells are needed to avoid false negative results, ii) overlapping results can be achieved using either PB or BM cell samples, iii) all CML patients were properly diagnosed at the onset of the disease, iv) CML patients in follow-up showing detectable fusion protein (i.e. rMFI% >1) revealed levels of BCR-ABL1IS transcripts between 1–10%, and v) rMFI% levels predict CCyR as defined by FISH analysis. Here, BCR is linked to chronic myelogenous leukemia, BCR-ABL1 positive.