Objectives <p>To evaluate the associations between anemia, anthropometry, and nutrient intake, considering the relationship between intestinal pathogen load and biomarkers of intestinal inflammation in the first two years of life.</p> Methods <p>Brazilian children in the MAL-ED cohort at 7 mo (<i>n</i> = 118), 15 mo (<i>n</i> = 132), and 24 mo (<i>n</i> = 127) of age were assessed. Markers of iron status, nutritional status, pathogen load in non-diarrheal stool samples, and fecal biomarkers of intestinal inflammation were analyzed. Usual nutrient intake was estimated using 24-h recalls, which were applied monthly. Two logistic regression models elucidated factors associated with anemia and iron-deficiency anemia.</p> Results <p>Anemia decreased over the period studied. Anemic children had lower weight-for-age z-scores (WAZ) and height-for-age z-scores (HAZ) at the 7th mo but at 15 mo, higher WAZ and weight-for-height z-scores (WHZ). The total load of pathogens decreased over the studied periods. Hemoglobin (Hb) was negatively correlated with intestinal inflammation and positively correlated with vitamin B12 intake. Children with higher WAZ presented a higher risk of anemia, and male children presented a higher risk of iron-deficiency anemia.</p> Conclusions <p>Anemia was significantly related to markers of inflammation. Thus, nutritional surveillance can be improved in children with anemia. Additional studies are needed to address measures to reduce intestinal inflammation as one strategy to combat anemia in children in the first two years of life.</p>