We used the World Health Organization's recommended procedures to establish desirable fortificant levels for three problem micronutrients in children's diets, based on dietary data collected earlier from Filipino (n = 1374; 6–36 months), Mongolian (n = 179; 12–36 months) and Cambodian (n = 177; 12–36 months) children. Prevalence of inadequate and excessive intakes of calcium and zinc (via cut-point method) and iron (via full-probability approach) was assessed after adjusting usual intake distributions with pc-side using internal or external within-person variances from Filipino (calcium and iron) and US National Health And Nutrition Examination Survey III (zinc) national surveys. Fortificant levels were determined by repositioning usual intake distributions so that the 2.5th percentile of the targeted populations equalled the estimated average requirement (calcium, zinc) or so that full-probability prevalence was no larger than 2.5% (iron). Prevalence of inadequate intakes was ≥70% for calcium and iron, except Filipino infants (30% for Ca) and Cambodian toddlers (41% for Fe); but <1% for zinc for toddlers in Mongolia and 20% in Cambodia. Prevalence of excessive intakes was <1% for zinc, calcium and iron, except for Mongolian toddlers (11% for Zn). Desirable fortificant levels, although apparently negligible for zinc, were 530–783 mg for calcium and 10.8–22.8 mg for iron (per 100 g). Fortificant levels can be estimated from 24-h recalls, preferably by applying internal within-person variances. Fortification with calcium and iron was necessary, but seemingly not for zinc, despite a high prevalence of low serum zinc, suggesting the need for better defined cut-offs for population risk of zinc deficiency based on dietary zinc intake and/or serum zinc.