Inadequate macro-and micronutrient nutrition and its consequences, such as anaemia, iron and vitamin deficiency, and growth retardation, could particularly affect children of small-scale farmers. In the present cross-sectional study, 666 school children aged 5–10 years from villages of Chamwino and Kilosa districts were studied for associations between nutritional and micronutrient status and dietary intake. The overall prevalence of stunting, underweight, and overweight was 28.1, 14.4, and 5%, while that of anaemia and deficiency of iron (ID), vitamin A (VAD), and zinc (ZnD) was 42.9, 29.3, 24.9, and 32.8%, respectively. Dietary recalls (24h) revealed that, except of iron (74%), only small proportions of children reached the recommended daily micronutrient intakes: 4% for zinc, 19% for vitamin A, and 14–46% for B vitamins. Stunting was highly associated with wasting in both districts and with VAD in Chamwino. Anaemia was predicted by ID, VAD, and ZnD in Chamwino and by elevated infection markers, C-reactive protein (CRP) and α-1 glycoprotein (AGP), in Kilosa. Overall, elevated CRP and/or AGP increased the risk while higher serum carotenoids indicating a diet of more fruit and vegetables reduced the risk of VAD. The significantly lower prevalence of anaemia and ID in Chamwino was related to higher iron and vitamin A intake and the consumption of mainly bulrush millet with dark green leafy vegetables compared to maize or rice with legumes in Kilosa. Nutrition and hygiene education integrated with home and school garden programmes could reduce the multiple burdens of anaemia; micronutrient deficiencies and infections; and, in the long term, the prevalence of stunting.
