Hidden hunger occurs in the presence of an otherwise nutritionally or energetically appropriate diet that is deficient in essential vitamins and minerals. Guatemala has the highest rate of child malnutrition in Latin America and the prevalence of hidden hunger is high. The aim of this study was to determine the Mn, Se and Cr dietary intakes in Guatemalan institutionalised children (4–14 years), a population group at high risk of mineral deficiency. For this purpose, the contents of Mn, Se and Cr were analysed in a duplicate diet (for 7 consecutive days) by electrothermal atomisation-atomic absorption spectrophotometry following acid digestion. Mn, Se and Cr intakes from the duplicate diets were in the range of 1·3–2·31 mg/d, 58·7–69·6 µg/d and 6·32–27·57 µg/d, respectively. Mn and Cr values were below current recommended daily intakes. A cereal- and legumes-based diet is habitually consumed by this population. Local vegetables, fruits and nutritional supplements are included daily, but the consumption of fish, meat, eggs and dairy products is very infrequent or negligible. Mean daily energy intake from the 7-d diet was 8418·2 kJ (2012 kcal), with a macronutrient energy distribution of carbohydrates 69·4 %, proteins 12·3 % and fats 18·3 %. Correlations between Mn, Se and Cr intakes and energy and other nutrient intakes were also evaluated. The present findings will help establish new nutritional strategies for this and similar population groups.