The objective of this study was to determine the population prevalence and correlates of neonatal abstinence syndrome among neonates born to women on methadone, using a cross-sectional analysis of linked population health data. A total of 2941 live births to women actively on methadone at delivery were analysed over an 11-year period (1992 - 2002). Of these births, 796 neonates (27%) were diagnosed with an International Classification of Diseases - 9CM (ICD-9CM) or International Classification of Diseases ICD - 10AM (ICD-10AM) diagnosis related to neonatal withdrawal from exposure to opiates in utero (NAS). There were significant differences found between mothers whose neonates did and did not receive an International Classification of Diseases NAS-related diagnosis. Mothers of neonates with a NAS-related diagnosis had a higher number of previous pregnancies, were more likely to be indigenous, to smoke more heavily and were more likely to present for delivery unbooked. Neonates diagnosed with NAS were admitted to Special Care Nursery more often. NAS is diagnosed less frequently using International Classification of Diseases (ICD) codes than when using clinical scales measuring opiate-related neonatal withdrawal. This suggests that NAS may be under-represented in hospital morbidity databases that use ICD codes to quantify patient throughput and in some circumstances this may result from under-detection of the condition. Future research should therefore seek to determine the validity of NAS recording in hospital morbidity databases reliant on the use ICD codes.