AimsWe aimed to investigate the impact of various genetic polymorphisms affecting thiopurine metabolism pathways and toxicity in paediatric acute lymphoblastic leukaemia patients for the first time in Korea.MethodsFrom May 2006 to September 2016, 139 paediatric acute lymphoblastic leukaemia patients treated with combination chemotherapy including 6‐mercaptopurine were included in the study. One hundred and twenty‐three variants in 43 genes, includingTMPTandNUDT15, were screened using targeted genotyping, such as a MassARRAY system, direct sequencing and polymerase chain reaction‐restriction fragment length polymorphism methods. Among the polymorphisms screened, 103 polymorphisms of 43 genes were included for further analyses.ResultsThe genetic polymorphisms in theABCC4,AHCY,ATIC,FAM8A6P,GART,GNG2,GSTA1,MTHFD1,MTHFR,NUDT15,PACSIN2,TYMSandXDHgenes, and an intronic polymorphism betweenHIVEP2andAIG1, andTPMTgenotype were associated with thiopurine metabolism (P < 0.05). Genetic polymorphisms in theABCC4,ADK,ATIC,GART,GMPS,GSTP1,IMPDH1,ITPA,KCNMA1,MOCOS,MTRR,NUDT15,SLC19A1,SLC28A3,SLC29A1,SLCO1B1,TYMPandXDHgenes were associated with thiopurine‐related toxicities; neutropenia, hepatotoxicity and treatment interruption (P < 0.05).ConclusionsFindings of this study may provide basic knowledge for personalized medicine for thiopurinxe treatment in paediatric acute lymphoblastic leukaemia patients.