Inflammation confounds the interpretation of several micronutrient biomarkers resulting in estimates that may not reflect the true burden of deficiency. We aimed to assess and compare the micronutrient status of a cohort of Indonesian infants (n 230) at aged 6, 9 and 12 months by ignoring inflammation (unadjusted) and adjusting four micronutrient biomarkers for inflammation with C-reactive protein (CRP) and α-1-glycoprotein (AGP) using the following methods: (1) arithmetic correction factors with the use of a four-stage inflammation model; and (2) regression modelling. Prevalence of infants with any inflammation (CRP>5 mg/l and/or AGP>1 g/l) was about 25% at each age. Compared with unadjusted values, regression adjustment at 6, 9 and 12 months generated the lowest (P<0·001) geometric mean (GM) for serum ferritin (26·5, 14·7, 10·8 μg/l) and the highest GM for serum retinol-binding protein (0·95, 1·00, 1·01 μmol/l) and Zn (11·8, 11·0, 11·5 μmol/l). As a consequence, at 6, 9 and 12 months regression adjustment yielded the highest prevalence of Fe deficiency (20·3, 37·8, 59·5 %) and the lowest prevalence of vitamin A (26·4,16·6, 17·3 %) and Zn (16·9, 20·6, 11·0 %) deficiency, respectively. For serum Se, irrespective of adjustment, GM were low (regression: 0·73, 0·78, 0·81 μmol/l) with prevalence of deficiency >50 % across all ages. In conclusion, without inflammation adjustment, Fe deficiency was grossly under-estimated and vitamin A and Zn deficiency over-estimated, highlighting the importance of correcting for the influence of such, before implementing programmes to alleviate micronutrient malnutrition. However, further work is needed to validate the proposed approaches with a particular focus on assessing the influence of varying degrees of inflammation (i.e. recurrent acute infections and low-grade chronic inflammation) on each affected nutrient biomarker.