The purpose of this study was to examine the relationship between social worker reports and the fatty acid ethyl ester (FAEE) test as a biomarker for heavy alcohol use. In 2005, a diagnostic program to detect excessive alcohol use by FAEE hair analysis in parents at high risk of having children with fetal alcohol spectrum disorders was established. All cases submitted by Child Protective Services between May and December of 2007 (n = 172) were included comparing social worker reports with FAEE test outcome by odds ratio analysis. A subanalysis of mothers (n = 119), excluding fathers, was also performed. Factors associated with testing positive for hair FAEE in parents, and mothers alone, were: knowledge of a specific instance of problem drinking within the past 6 months (odds ratio [OR] = 5.11, 2.57-10.16 and OR = 8.51, 3.59-20.18, respectively) and third party reports alleging alcohol abuse (OR = 3.31, 1.69-6.46 and OR = 3.30, 1.45-7.50, respectively). Mothers who admitted to heavy drinking were also seven times more likely to test positive for hair FAEE (OR = 6.74, 1.50-30.38) than those who did not. Factors negatively associated with testing positive for hair FAEE in parents, and mothers alone, were: social workers testing for FAEE without the suspicion of alcohol use but rather as a measure to "cover all bases" (OR = 0.09, 0.02-0.40 and (OR = 0.13, 0.03-0.58, respectively) or because of a history/suspicion of illicit drug use (OR = 0.2, 0.07-0.55 and OR = 0.26, 0.08-0.80, respectively). Eleven of 15 reports, indicating levels of consumption, were also in clinical agreement with FAEE test outcome. The FAEE hair test is being applied for the first time in the present context. Our results show the test corroborates well with social workers' suspicion of alcohol use. Reported factors directly related to alcohol use were significantly associated with testing positive for excessive alcohol use, whereas factors not directly related to alcohol use were negatively associated with testing positive.