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Summary: We performed a retrospective analysis of leukaemic surface antigen expression and genomic data from a total of 100 RUNX1‐RUNX1T1–positive paediatric acute myeloid leukaemia (AML) patients enrolled in the Japanese Paediatric Leukaemia/Lymphoma Study Group (JPLSG) AML‐05 protocol to determine risk factors for relapse. In univariate analysis, the KIT exon 17 mutation (n = 21) and CD19 negativity (n = 59) were significant risk factors for relapse (P = 0·01). In multivariate analysis, CD19 negativity was the sole significant risk factor for relapse (hazard ratio, 3·09; 95% confidence interval, 1·26–7·59; P < 0·01), suggesting that biological differences between CD19‐positive and CD19‐negative RUNX1‐RUNX1T1 AML patients should be investigated. [ABSTRACT FROM AUTHOR]