Objective: The aims of the current study were to determine whether children with the 6 different APOE e genotypes show differences in gray matter maturation, particularly for those with e4 and e2 alleles, which are associated with poorer outcomes in many neurologic disorders.Methods: A total of 1,187 healthy children (aged 3-20 years, 52.1% boys, 47.9% girls) with acceptable data from the cross-sectional Pediatric Imaging Neurocognition and Genetics Study were evaluated for the effects of 6 APOE e genotypes on macroscopic and microscopic cortical and subcortical gray matter structures (measured with 3-tesla MRI and FreeSurfer for automated morphometry) and on cognition (NIH Toolbox).Results: Among APOE e4 carriers, age-related changes in brain structures and cognition varied depending on genotype, with the smallest hippocampi in e2e4 children, the lowest hippocampal fractional anisotropy in younger e4e4 children, the largest medial orbitofrontal cortical areas in e3e4 children, and age-dependent thinning of the entorhinal cortex in e4e4 children. Younger e4e4 children had the lowest scores on executive function and working memory, while younger e2e4 children performed worse on attention tasks. Larger parietal gyri in the younger e2e4 children, and thinner temporal and cingulate isthmus cortices or smaller hippocampi in the younger e4e4 children, predicted poorer performance on attention or working memory.Conclusions: Our findings validated and extended prior smaller studies that showed altered brain development in APOE e4-carrier children. The e4e4 and e2e4 genotypes may negatively influence brain development and brain aging at the extremes of age. Studying APOE e polymorphisms in young children may provide the earliest indicators for individuals who might benefit from early interventions or preventive measures for future brain injuries and dementia. Neurology ® 2016;87:585-594 GLOSSARY AD 5 Alzheimer disease; FA 5 fractional anisotropy; GAF 5 genetic ancestry factor; GAM 5 general additive model; PING 5 Pediatric Imaging, Neurocognition, and Genetics; ROI 5 region of interest; SES 5 socioeconomic status; WM 5 working memory.