A serious challenge in diagnosing fetal alcohol spectrum disorder (FASD) is the need to document alcohol use during pregnancy. Maternal/paternal alcohol abuse affects the likelihood of fetal alcohol exposure, and hence the occurrence of FASD. The objective of the current study was to document the use of the fatty acid ethyl ester (FAEE) hair test, a biomarker of excessive alcohol use, in parents at risk of having children with FASD and quantify the prevalence of alcohol use in this population. Hair samples submitted for FAEE testing between October 2005 and May 2007 were evaluated (n = 324). Subjects consisted of the parents of at-risk children. Samples were analyzed using a previously published method. Briefly, samples underwent a liquid-liquid extraction, followed by headspace solid phase microextraction, and were then analyzed by gas chromatography-mass spectrometry using deuterated FAEE as internal standards. Limit of detection and limit of quantification values were between 0.01-0.04 ng/mg and 0.04-0.12 ng/mg, respectively. Positive levels for excessive drinking were ascertained using a cutoff level of 0.5 ng/mg, offering 90% sensitivity and specificity. The rate of positive hair samples for excessive drinking was 33.3% (32.4% among women and 35.4% among men) (n = 324). The majority of samples (62%) had cumulative FAEE levels above a level that excludes strict abstinence (0.2 ng/mg) and many (19%) were highly positive (above 1.0 ng/mg). Of 26 FAEE hair tests for which women were reported to be pregnant, 38% had FAEE hair levels above 0.2 ng/mg and 19% tested positive for excessive drinking, with levels above 0.5 ng/mg; 12% had levels above 1.0 ng/mg. The high rate of positive FAEE results demonstrates that the FAEE hair test corroborates the clinical suspicion of alcohol use in parents of children at risk for FASD. Our results suggest that FAEE hair analysis may be a powerful tool in detecting excessive alcohol use in the perinatal period.