Many common childhood conditions are associated with cognitive deficits. While some causes of impaired cognition, such as lead exposure, are well understood, other common conditions in countries such as Uganda – malnutrition, anemia and malaria – are not sufficiently recognized. In this chapter we discuss stunting and its root causes of undernutrition, a lack of sanitation and its relationship to environmental enteropathy and the intestinal microbiome. We also review information about iron-deficiency anemia and malaria, and their neurological and cognitive consequences. We believe that cognitive declines later in life, during adulthood, may be prevented or delayed by addressing these childhood threats to cognition.