The pattern of molecular response is mirrored by the corresponding cytogenetic response. (A) The patient crossed over to imatinib after interferon-α failure and a rise in BCR-ABL (Ai) was associated with the detection of a consistently minor mutated clone. Corresponding bone marrow (BM) cytogenetic analysis (Aii) revealed loss of complete cytogenetic response (CCR) and a duplicate Ph. Interestingly, after an autologous transplantation the mutation was not detected. However, the duplicate Ph was present at loss of response, which possibly indicates that the minor mutated clone was eradicated at transplantation. This case illustrates the importance of cytogenetic analysis after loss of molecular response. (B) The patient had a typical rapid and sustained response to first-line imatinib. Molecular analysis (Bi) showed that BCR-ABL remained detectable for more than 2 years after CCR was documented at 6 months (Bii). This case illustrates that cytogenetic analysis may be of no clinical benefit while the patient maintains molecular response.