Studies in adults have shown that an early molecular response to imatinib predicts clinical outcome in chronic myeloid leukemia (CML). We investigated the impact of the BCR-ABL1 transcript level measured 3 months after starting imatinib in a cohort of 40 children with CML. Children with a BCR-ABL1/ABL ratio higher than 10% at 3 months after the start of imatinib had a larger spleen size and a higher white blood cell count compared with those with BCR-ABL1/ABL ≤10%. Children with BCR-ABL1/ABL ≤10% 3 months after starting imatinib had higher rates of complete cytogenetic response and major molecular response at 12 months compared to those with BCR-ABL1/ABL \textgreater10%. With a median follow-up of 71 months (range: 22 to 96), BCR-ABL1/ABL ≤10% correlated with better progression free survival. Thus, early molecular response at 3 months predicts outcome in children treated with imatinib for CML. The study was registered at www.clinicaltrials.gov as NCT00845221.