Reliance on self-reported use of tobacco and intake of ethanol during pregnancy is associated with a high probability of error. Use of biological markers, or biomarkers, potentially offers a more valid method to assess exposure. Although cotinine is an established biomarker for tobacco use, there is no established biomarker for in utero ethanol exposure. Recent reports suggest that fatty acid ethyl esters (FAEE) could serve this purpose. To assess agreement between maternal self-reported tobacco use and ethanol intake during pregnancy and detection of metabolites associated with tobacco use (cotinine) and ethanol intake (FAEE), the authors studied maternal histories and meconium samples obtained in November-December 1999 from 436 consecutive mother-infant pairs at a large urban regional perinatal center in Honolulu, Hawaii. Cohen's kappa coefficient and 95% confidence intervals were calculated. Moderate agreement was found between reported tobacco use during the third trimester and detected cotinine level (kappa = 0.53, 95% confidence interval: 0.39, 0.68); however, there was no agreement between reported ethanol intake during the third trimester and detected FAEE (kappa = -0.02, 95% confidence interval: -0.04, 0.00). No mother reporting ethanol intake during the third trimester had detectable FAEE. Findings support the need for additional refinement and validation of the use of FAEE as a biomarker for maternal ethanol intake.