The European Food Safety Authority (EFSA) received a request from the European Commission for a scientific opinion on perchlorate in food, in particular fruits and vegetables. Perchlorate is a contaminant released into the environment from both natural and anthropogenic sources. The use of natural fertilisers and perchlorate contaminated irrigation water may lead to substantial concentrations in leafy vegetables. Water disinfection with chlorinated substances that potentially degrade to perchlorate could be another potential source of contamination. EFSA received analytical results for 11 675 samples submitted by eight Member States, mainly for fruits, vegetables, and fruit and vegetable products. The EFSA Panel on Contaminants in the Food Chain (CONTAM Panel) performed estimates of both chronic and ‘short-term’ exposure considering the available dataset, and data from the literature on the levels of perchlorate in fruit juices, alcoholic beverages, milk, infant formulae and breast milk. The CONTAM Panel established a tolerable daily intake of 0.3 µg/kg body weight per day, based on the inhibition of thyroid iodine uptake in healthy adults. Amongst the vulnerable subpopulations, potential acute effects of perchlorate have been suggested for fetuses and infants. The CONTAM Panel noted that a single acute exposure to perchlorate at levels found in food and water is unlikely to cause adverse effects on human health, including the more vulnerable groups of the population, and concluded that the establishment of an acute reference dose for perchlorate is not warranted. Overall, the CONTAM Panel concluded that the chronic dietary exposure to perchlorate is of potential concern, in particular for the high consumers in the younger age groups of the population with mild to moderate iodine deficiency. Furthermore, it is possible that exposure to perchlorate is of concern for infants breast-fed by iodine-deficient mothers.