Sugar-free confectionery products containing the low-energy, non-cariogenic sweetener isomalt are widely available in the market place and increasingly aimed at children. However, over-consumption of such products may lead to gastrointestinal symptoms and/or osmotic diarrhoea. Little is known about the gastrointestinal tolerance of children following consumption of isomalt. The aim of the present study was to assess gastrointestinal symptoms in children following consumption of sugar-free confectionery containing isomalt compared with sweets containing sucrose. In a double-blind, randomised, controlled, crossover study, sixty-seven children aged 6–9 years ingested 25 g hard-boiled sweets containing either sucrose or isomalt on two consecutive test days. Isomalt sweets were received as enthusiastically as sucrose sweets and, when given the choice, 97 % of children asked to be given the isomalt or the sucrose sweets on the second test day. Most children did not report multiple symptoms and few experienced symptoms on both days of isomalt consumption. However, significantly more children reported stomach-ache (P<0·01), abdominal rumbling (P<0·025) and passing watery faeces (P<0·001) following consumption of isomalt sweets compared with sucrose sweets. Consumption of 25 g isomalt-containing sweets by children is not associated with significant gastrointestinal effects graded as ‘considerably more than usual’ or multiple symptoms, but is associated with a laxative effect and increase in symptoms graded as ‘slightly more than usual’. For the majority of children in the present study, 25 g isomalt-containing sweets represents an acceptable level of consumption, although some children are sensitive to the effects of isomalt ingestion.