Multiple micronutrient deficiencies (MNDs) co-exist, often because of poor intakes and adversely impact health. Habitual diets were assessed in 300 school children (6-17 years old) recruited from two government schools by simple random sampling. Probability of adequacy (PA) for 11 micronutrients and mean probability of adequacy (MPA) was calculated. Haemoglobin, plasma ferritin, folic acid, vitamin B and C-reactive protein were estimated. Descriptive statistics and regression analysis were used to estimate magnitude and factors associated with MNDs. The contribution of fortified foods and/or supplements in addressing inadequacies and excessive intakes was modelled. The PA ranged from 0.04 for folate to 0.70 for zinc, and the MPA was 0.27. Prevalence of anaemia (53%), iron deficiency (57%; ID), iron deficiency anaemia (38%; IDA), folate deficiency (24%) and B deficiency (43%) was high. Dietary inadequacy of iron, zinc and a low MPA was associated with anaemia and IDA. Inclusion of double fortified salt (DFS), fortified rice (FR) or iron folic acid (IFA) supplements individually in habitual diet reduced probability of iron inadequacy significantly from 82% to ≤13%. Inclusion of DFS and FR simultaneously led to disappearance of iron inadequacy, but risk of excessive intake increased to 16%. Inclusion of DFS, FR and IFA together increased risk of excess iron intake to 40%. Nevertheless, intakes of folate and B remained inadequate even with FR and/or IFA. These results indicate a high risk of dietary MNDs in children and suggest need for more systematic intake measurements in representative sample and adjustment of iron dosages to avoid excessive intakes.