| Summary: | Multiple common variants in <i>transmembrane protease serine 6 (TMPRSS6)</i> were associated with the plasma iron concentration in genome-wide association studies, but their effect in young children where anemia and iron deficiency (ID) were prevalent has not been reported, particularly taking account of iron intake. This study aims to investigate whether <i>TMPRSS6</i> SNPs (rs855791 and rs4820268) and iron intake are associated with a low iron and hemoglobin concentration in under-two-year-old children. The study analyzed the baseline of a randomized trial (NUPICO, ClinicalTrials.gov NCT01504633) in East Lombok, Indonesia. Children aged 6–17 months (<i>n</i> = 121) were included in this study. The multiple linear regressions showed that <i>TMPRSS6</i> decreased serum ferritin (SF) by 4.50 g/L per copy minor allele (A) of rs855791 (<i>p</i> = 0.08) and by 5.00 μg/L per copy minor allele (G) of rs4820268 (<i>p</i> = 0.044). There were no associations between rs855791 and rs4820268 with soluble transferrin receptor (sTfR) and hemoglobin (Hb) concentration (rs855791; <i>p</i> = 0.38 and <i>p</i> = 0.13, rs4820268; <i>p</i> = 0.17 and <i>p</i> = 0.33). The finding suggests the need for further studies to explore whether the nutrient recommendation for iron should be based on genetic characteristics, particularly for children who have mutation in <i>TMPRSS6</i>.
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