Background/Aim: Droplet digital polymerase chain reaction (ddPCR) is an exact method of measuring nucleic acids. The aim of this prospective study was to evaluate minimal residual disease (MRD) using ddPCR in chronic myeloid leukemia (CML) patients. Patients and Methods: Between May 2013 and November 2014, CML patients treated with nilotinib were enrolled in our study. BCR/ABL1 transcripts levels were evaluated using ddPCR at the first time of complete molecular response (CMR). We enrolled 15 patients from 7 Institutions. The treatment period and median follow-up period were 45 months and 47 months, respectively. Results: Patients with a high level of BCR/ABL1 transcript had a greater tendency to lose the CMR during the follow-up period (p=0.095). In addition, patients with a low level of BCR/ABL1 transcript showed a longer duration of CMR compared to those with a high level (p=0.032). Conclusion: We found that ddPCR is a sensitive method for detecting MRD and that MRD could affect the duration of the treatment response. Chronic myeloid leukemia (CML) is cytogenetically characterized by the translocation of t(9; 22) (q34;q11.2), which produces the BCR/ABL1 fusion oncogene (1). Since the success of imatinib, the first targeted agent in human history, more effective tyrosine kinase inhibitors (TKIs), such as dasatinib and nilotinib have been introduced to the frontline treatment of CML and show a 76-82% major molecular response rate (2, 3). CML is now thought to be a lifelong disease with a 5-year overall survival rate>90% (4). Previous reports have demonstrated that achievement of an early molecular response is a strong predictive marker of improved outcomes (5). Therefore, the European LeukemiaNet 2273 This article is freely accessible online.