Patients having inborn errors of intermediary metabolism (IEMs) may have element deficiencies related to dietary treatment. Our objective was to study several elements [cobalt (Co), copper (Cu), zinc (Zn), selenium (Se), manganese (Mn), molybdenum (Mo) and magnesium (Mg)] in patients with IEMs with and without dietary treatment and to compare these results with those established in a healthy paediatric population. We studied 72 patients with IEMs (age range 2 months-44 years; median 10.5 years), with and without protein-restricted dietary treatment. Control values were established in 92 subjects (age range 1 day-42 years; median 6.5 years). Dietary treatment consisted of a natural protein-restricted diet supplemented with a special formula, depending on the specific metabolic defect. Samples were analysed with an Agilent 7500ce-ICP mass spectrometer. Significant differences were observed when we compared patients under dietary treatment and control values for Se and Co (P < 0.0001). No differences were observed for the other elements when the different groups were compared, except for Co (IEM patients without dietary treatment vs control group; P = 0.003). For Se and cobalamin, the daily intake of our patients (Se 48 ± 16 µg/day; cobalamin 3.5 µg/day) was slightly higher than the recommended daily averages (RDAs) (40 µg/day and 1.8 µg/day, respectively). We concluded that IEM patients under dietary treatment showed significantly lower selenium values in spite of correct supplementation, reinforcing the idea that these patients should be regularly monitored, at least for this element. Further investigations seem advisable about Se and Co availability in special diets.