Fatty acid ethyl esters (FAEEs) in meconium are validated biomarkers of heavy fetal alcohol exposure that may potentially be used clinically for identifying children at risk for alcohol-related disabilities. However, until now, FAEEs have been largely used anonymously in epidemiological studies, and by child protection authorities in need for verification of heavy alcohol use in pregnancy. Here we describe the first case of a neonate identified as part of a research study on a pilot neonatal screening program for prenatal alcohol exposure. The neonate's meconium tested high for FAEEs (52 nmol/g; positive cut-off ≥ 2 nmol/g), which prompted active follow-up of the infant's development, identifying early neurocognitive problems and allowing initiation of a remedial program.