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Approval for glyphosate-based herbicides in the European Union (EU) is under intense debate due to concern about their effects on the environment and human health. The occurrence of glyphosate residues in European water bodies is rather well documented whereas only few, fragmented and outdated information is available for European soils. We provide the first large-scale assessment of distribution (occurrence and concentrations) of glyphosate and its main metabolite aminomethylphosphonic acid (AMPA) in EU agricultural topsoils, and estimate their potential spreading by wind and water erosion. Glyphosate and/or AMPA were present in 45% of the topsoils collected, originating from eleven countries and six crop systems, with a maximum concentration of 2 mg kg− 1. Several glyphosate and AMPA hotspots were identified across the EU. Soil loss rates (obtained from recently derived European maps) were used to estimate the potential export of glyphosate and AMPA by wind and water erosion. The estimated exports, result of a conceptually simple model, clearly indicate that particulate transport can contribute to human and environmental exposure to herbicide residues. Residue threshold values in soils are urgently needed to define potential risks for soil health and off site effects related to export by wind and water erosion.