To examine associations between amounts of fatty acid ethyl esters (FAEEs) in meconium and cognitive development in school-aged children exposed to alcohol and drugs in utero. A secondary analysis of a prospective cohort of children, primarily African American and of low socioeconomic status, that was recruited at birth. FAEEs were quantified with gas chromatography via a flame ionization detector. Meconium was analyzed for FAEEs in 216 newborns; 191 of these infants were assessed for IQ at ages 9, 11, and 15 years with the Wechsler Intelligence Scales for Children-Fourth Edition. Longitudinal mixed model analyses indicated that, after we controlled for maternal and child covariates, greater concentrations of FAEEs (ethyl myristate, ethyl oleate, ethyl linoleate, and ethyl linolenate) were associated with lower Wechsler Intelligence Scales for Children-Fourth Edition Verbal Comprehension Index, Working Memory Index, and Full-Scale IQ scores. Associations of FAEEs with Verbal Comprehension Index, Working Memory Index, and Full-Scale IQ did not vary over time. No associations of FAEEs with Perceptual Reasoning and Processing Speed Indices were found. Elevated levels of FAEEs in meconium are potential markers for identifying newborns at risk for poor cognitive development related to prenatal alcohol exposure.