Due to the toxic effect of Aflatoxin (AF), the European Union has implemented strict standards regarding its maximum acceptable levels in tree nuts and peanuts. This paper evaluates the impact of changes in AF standards, a lessening of the maximum residue levels on the frequency of border controls. To do that, a count data model was proposed and estimated to test the determinants of border controls on EU imports of these products, based on political economy considerations, past alerts, path dependence effects and other scientific and economic variables. The revision of these standards has involved changes in controls and border refusals as measured by notifications at the Rapid Alert System for Food and Feed. Changes in AF standards are estimated to have significant impact on the frequency of border controls.