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Minimal residual disease (MRD) is of high prognostic value in risk stratification in childhood acute lymphoblastic leukaemia. Flow cytometry (FCM) was shown to yield reliable results in MRD measurement. However, the interpretation of FCM data relies largely on operator skills and experience. While sample preparation, antibody panels, staining procedures and flow cytometric acquisition can be standardized, easily controlled and be made available worldwide, the availability of experienced operators represents the current bottleneck to a growing number of laboratories to the benefit of an increasing number of patients with leukaemia. Currently, international paediatric studies—throughout Europe, South America, to Australia—aim at stratifying the treatment according to the FCM-MRD methodology. The measurements are still operator-dependent leading to substantial costs regarding training and quality control. This article introduces a new European Union-funded project (AutoFLOW) aiming at the standardization and automation of FCM-MRD analysis by machine-learning technology.