Background: Iron deficiency anemia and feeding difficulties (FD) are common issues in childhood, reinforcing the concern about the risk of micronutrient deficiencies. FD do not necessarily reflect nutritional deficiencies, since they may or may not relate to specific nutrient sources. The objective of the study is to describe the prevalence of iron depletion and iron deficiency anemia in children with FD and to seek associations with diagnosis and its markers. Methods: This is a cross-sectional study with 68 patients (convenience sample). The following data were assessed through medical records: age (months), gender, exclusive breastfeeding duration (months), birth weight (kg), iron supplementation, hemoglobin (Hb), ferritin, and C-reactive protein (CRP) levels, repertory of foods consumed (food inventory and 3-day food record analysis), and diagnosis of FD. Data were classified according to references for age and were analyzed using correlation tests, Student's t test, ANOVA and chi-square test, or its nonparametric equivalents. A significance level of 5% was considered. Results: Iron depletion and anemia were identified in 10.1 and 6% of children, respectively. Picky eating was diagnosed in 35.3%. Food repertory consisted on average of 21 foods, with null correlation to Hb and ferritin. The average fortified milk intake was 517 ml/day, with null correlation to Hb. There was no effect of diagnosis of FD on Hb (p = 0.18) or ferritin (p = 0.52). The same was verified in the children without supplementation, to both Hb (p = 0. 54) and ferritin (p = 0.08). Conclusions: No evidence of association between diagnosis of FD or repertory of foods to anemia or iron depletion was found, which could be a reassuring factor for caregivers. Reproduction in large scale as well as inclusion of dietary intake variables is suggested for further research.