Introduction: According to the World Health Organization (WHO), anemia is a severe public health problem when the prevalence is ≥ 40%. In 2019, in Peru, 40.1% of children (age 6 to 35 months) are diagnosed as anemic. This is a concern since, despite the efforts of the governments to reduce the prevalence, the problem has stagnated since 2011. The treatment applied to deal with anemia is iron supplementation. Although iron is essential for cell function, an excess can produce adverse responses, such as gut inflammation affecting microbiota and resulting in diarrheic episodes. Objective: To determine the association between diarrhea and iron supplementation in children with and without anemia, controlling for different socio-demographic variables. Design: We conducted via logistic regression to obtain diarrhea prevalence ratios, adjusted by age, sex, geographic region, water and sanitation service, and rurality. The survey asked for recent episodes of diarrhea during the last 7 days; similarly, after the consumption of iron supplements during the last 12 months before the survey. Setting: Peru Subjects: The Demographic and Health Survey (DHS) is conducted annually at home among 14,202 children on average (2009 - 2019). Results: Iron supplementation in the last seven days (PR=1.09) or the last twelve months (PR=1.19) (p<0.0001) was associated with an increased risk of diarrhea. The same association was observed between iron supplementation and the presence of anemia. Conclusions: Iron supplementation is associated with diarrhea and over-use in children should be avoided.