© 2015 by American Society of Clinical Oncology. Purpose: Mercaptopurine (MP) is the mainstay of curative therapy for acute lymphoblastic leukemia (ALL).We performed a genome-wide association study (GWAS) to identify comprehensively the genetic asis of MP intolerance in children with ALL. Patients and Methods: The discovery GWAS and replication cohorts included 657 and 371 children from two prospectivec linical trials. MP dose intensity was a marker for drug tolerance and toxicities and was defined as prescribed dose divided by the planned protocol dose during maintenance therapy; its association with genotype was evaluated using a linear mixed-effects model. Results: MP dose intensity varied by race and ethnicity and was negatively correlated with East Asian genetic ancestry (P < .001). The GWAS revealed two genome-wide significant loci associated with dose intensity: rs1142345 in TPMT (Tyr240Cys, present in∗3A and∗3C variants; P = 8.6∗10-9) and rs116855232 in NUDT15 (P = 8.8∗10-9), with independent replication. Patients with TT genotype at rs116855232 were exquisitely sensitive to MP, with an average dose intensity of 8.3%, compared with those with TC and CC genotypes, who tolerated 63% and 83.5% of the planned dose, respectively. The NUDT15 variant was most common in East Asians and Hispanics, rare in Europeans, and not observed in Africans, contributing to ancestry-related differences in MP tolerance. Of children homozygous for either TPMT or NUDT15 variants or heterozygous for both, 100% required ≤ 50% MP dose reduction, compared with only 7.7% of others. Conclusion: We describe a germline variant in NUDT15 strongly associated with MP intolerance in childhood ALL, which may have implications for treatment individualization in this disease.