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 -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<bold></bold>001) geometric mean (GM) for serum ferritin (26<bold></bold>5, 14<bold></bold>7, 10<bold></bold>8 g/l) and the highest GM for serum retinol-binding protein (0<bold></bold>95, 1<bold></bold>00, 1<bold></bold>01 mol/l) and Zn (11<bold></bold>8, 11<bold></bold>0, 11<bold></bold>5 mol/l). As a consequence, at 6, 9 and 12 months regression adjustment yielded the highest prevalence of Fe deficiency (20<bold></bold>3, 37<bold></bold>8, 59<bold></bold>5 %) and the lowest prevalence of vitamin A (26<bold></bold>4,16<bold></bold>6, 17<bold></bold>3 %) and Zn (16<bold></bold>9, 20<bold></bold>6, 11<bold></bold>0 %) deficiency, respectively. For serum Se, irrespective of adjustment, GM were low (regression: 0<bold></bold>73, 0<bold></bold>78, 0<bold></bold>81 mol/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.