Background: Opioid and cocaine antenatal substance use can result in significant obstetric and pediatric health implications. Accurate detection of in utero-exposed neonates can improve patient care and health outcomes. Therefore, the effectiveness of mother-infant biological and diagnostic indicators collected at labor and delivery to provide accurate detection of in utero opiate and cocaine exposure was assessed. Methods: A retrospective medical chart review included 335 mother-infant dyads exposed to antenatal substances who were delivered between January 2009 and March 2014. Mother-infant dyads were a subset of a larger retrospective cohort of 560 substance-using mothers, who had a valid meconium drug screen (MDS) and anesthesia before delivery. Alternative biological and diagnostic indicators of maternal urine drug screens (UDS), maternal substance use International Classification of Disease, Ninth Revision, Clinical Modification (ICD-9-CM) codes, and neonatal exposure diagnostic ICD-9-CM codes were compared against MDS. Data were analyzed using classification accuracy measures. Results: Compared with MDS, maternal UDS had the highest sensitivity [0.52, 95% confidence interval (CI), 0.39-0.65] and specificity (0.88, 95% CI, 0.79-0.97) to detect intrauterine opiate exposure. Maternal substance use diagnosis had the highest sensitivity (0.39, 95% CI, 0.16-0.61) and maternal UDS had the highest specificity (1.00, 95% CI, 0.99-1.00) to detect intrauterine cocaine exposure. Cocaine exposure had significantly higher accuracy scores across detection methods compared with opiate exposure. Conclusions: Alternative indicators collected at delivery were ineffective at identifying in utero substance exposure, especially neonatal-exposed ICD-9-CM codes. Low sensitivity scores indicate that many exposed neonates could be misdiagnosed or left untreated. Accurate antenatal exposure identification at delivery is an important form of tertiary assessment that warrants the development of improved screening methodology and standardization of hospital biological drug testing.