The most common mechanism of acquired resistance in CML in imatinib era is the acquisition of BCR-ABL kinase domain mutations with decreased sensitivity to the drug. At time of resistance, treatment of CML now involves sequential use of second generation tyrosine kinase inhibitors (TKIs). Persistence of pre-existing mutations, as well as development of new mutations is a mechanism of resistance to the new TKI. In-vitro, mutations can be low, intermediate or highly sensitive to the different TKIs. However the in-vitro testing may not translate to in-vivo results. In fact we describe the case of one patient, who never had any cytogenetic response, developed G250E mutation on imatinib (G250E in-vitro sensitivity good for nilotinib dasatinib and intermediate for imatinib) that persisted on nilotinib and dasatinib, and developed a V299L mutation while on dasatinib (in-vitro intermediate sensitivity). Another patient never achieved cytogenetic response, developed E355G mutation on imatinib (intermediate in-vitro sensitivity to imatinib) that persisted on nilotinib, and once switched to dasatinib developed F317L mutation (intermediate in-vitro sensitivity). These patients exemplify the complexities of resistance of TKI therapy and argue for the need to investigate mechanisms of resistance beyond mutations.