In Vietnam, nutrition interventions do not target school children despite a high prevalence of micronutrient deficiencies. The present randomised, placebo-controlled study evaluated the impact of providing school children (n 403) with daily multiple micronutrient-fortified biscuits (FB) or a weekly Fe supplement (SUP) on anaemia and Fe deficiency. Micronutrient status was assessed by concentrations of Hb, and plasma ferritin (PF), transferrin receptor (TfR), Zn and retinol. After 6 months of intervention, children receiving FB or SUP had a significantly better Fe status when compared with the control children (C), indicated by higher PF (FB: geometric mean 36·9 (95 % CI 28·0, 55·4) μg/l; SUP: geometric mean 46·0 (95 % CI 33·0, 71·7) μg/l; C: geometric mean 34·4 (95 % CI 15·2, 51·2) μg/l; P < 0·001) and lower TfR concentrations (FB: geometric mean 5·7 (95 % CI 4·8, 6·52) mg/l; SUP: geometric mean 5·5 (95 % CI 4·9, 6·2) mg/l; C: geometric mean 5·9 (95 % CI 5·1, 7·1) mg/l; P = 0·007). Consequently, body Fe was higher in children receiving FB (mean 5·6 (sd 2·2) mg/kg body weight) and SUP (mean 6·1 (sd 2·5) mg/kg body weight) compared with the C group (mean 4·2 (sd 3·3) mg/kg body weight, P < 0·001). However, anaemia prevalence was significantly lower only in the FB group (1·0 %) compared with the C group (10·4 %, P = 0·006), with the SUP group being intermediate (7·4 %). Children receiving FB had better weight-for-height Z-scores after the intervention than children receiving the SUP (P = 0·009). Vitamin A deficiency at baseline modified the intervention effect, with higher Hb concentrations in vitamin A-deficient children receiving FB but not in those receiving the SUP. This indicates that vitamin A deficiency is implicated in the high prevalence of anaemia in Vietnamese school children, and that interventions should take other deficiencies besides Fe into account to improve Hb concentrations. Provision of biscuits fortified with multiple micronutrients is effective in reducing anaemia prevalence in school children.