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Aiming at accelerating the implementation of cumulative risk assessment to pesticide residues, this report describes a two‐step prioritisation analysis, on individual pesticides and on target organ systems, that allows to identify (i) low‐priority substances expected to have a marginal contribution to cumulative risk, and (ii) high priority organ systems to be addressed in future cumulative risk assessments. The analysis encompassed 350 substances and 36 raw primary commodities of plant origin surveyed in the monitoring cycle 2019–2021, carried out in 30 population groups, covering 3 age classes, and 17 EU countries. Probabilistic exposure calculations, for chronic and acute effects, were executed on the occurrence and consumption data by a two‐dimensional procedure, modelling variability and uncertainty. In the first step, the prioritisation method adopted allowed to reduce the number of substances by about 80%. These substances were in turn grouped based on their capacity to cause toxicological effects on common organ systems and, as second step, probabilistic combined exposure calculations were carried out for 16 target organ systems. This step allowed to identify the organ systems that need further assessment, reducing their initial number by about 70%. The organ systems would need to be prioritised as follows: reproductive and developmental toxicity, liver, kidney, male reproductive system, and haematopoietic system and haematology. The sources of uncertainty stemming from the modelling procedure and from methodological assumptions were discussed and their impact qualitatively assessed. Overall, it was concluded that the risk estimates for the different organ systems were more likely to be overestimated than underestimated. [ABSTRACT FROM AUTHOR]