BackgroundWhen maternal micronutrient intakes and statuses are compromised, reductions in micronutrient concentrations in neonatal stores and human milk may result in suboptimal micronutrient intakes, statuses, and functional outcomes of breastfed infants during the critical first 6-month period. ObjectivesWe compared the adequacy of micronutrient intakes and statuses at 2 and/or 5 months and morbidity and growth faltering at 2, 5, and 12 months in a cohort of exclusively breastfed (EBF) and partially breastfed (PBF) infants from low-resource Indonesian households. MethodsAt 2 and 5 months, the breastfeeding status and human milk intake of 212 infants were determined using the deuterium oxide dose-to-mother technique, and intakes were calculated from milk micronutrient concentrations and 3-d weighed food intakes. At 5 months, five infant micronutrient biomarkers, hemoglobin, C-reactive protein, and α-1-acid-glycoprotein were measured. Infant morbidity, weight, and length were measured at 2, 5, and 12 months. Means, medians, or proportions were reported for each group and differences between groups were statistically determined. ResultsMedian intakes of iron, thiamin, niacin, and vitamin B-12 were higher in PBF than EBF infants at 5 months (all P values < 0.05), but intakes in all infants were below adequate intakes. At 5 months, anemia was <20% in both groups, although fewer PBF versus EBF infants had vitamin B-12 deficiency (11.5% vs. 28.6%, respectively; P = 0.011). The mean ± SD length-for-age z-scores for EBF versus PBF infants at 2 months were 0.7 ± 0.9 versus −0.5 ± 1.1, respectively (P = 0.158), declining to −1.4 ± 0.9 versus −1.1 ± 1.2, respectively, at 12 months (P = 0.059). Reported morbidity rates were generally low, with no evidence of a difference between infant groups (all P values > 0.126). ConclusionsIrrespective of exclusive or partial breastfeeding status, micronutrient intakes of infants were low, statuses were compromised, and growth faltering during the critical 6 months period of early infancy was present. The findings highlight the importance of improving maternal nutritional statuses and evaluating their impacts on infant outcomes.