Using a retrospective cross-sectional study design, we examined smoking patterns and associated neonatal outcomes in infants born to women with a diagnosis of a substance use disorder in pregnancy. Antenatal and birth admissions were linked to midwives data on pregnancy care, services, and outcomes over a 5-year period (1998-2002). Birth admissions were flagged as positive for drug use where a birth admission or any pregnancy admission for that birth involved a cannabis-, opioid-, stimulant-, or alcohol-related ICD-10AM code. There were 4,346 live births to women with a substance-related diagnosis in pregnancy. Women with a substance-related diagnosis (the drug group) had an adjusted odds ratio for smoking during pregnancy of 10.8 (95% CI = 9.9-11.7) relative to women without a substance-related diagnosis (the non-drug group). Women in the drug group also were heavier smokers; 26% smoked 1-10 cigarettes/day and 56% smoked more than 10 cigarettes/day compared with 8% in both groups in the non-drug group. Relative to the drug group, the adjusted odds ratio for quitting smoking during pregnancy in the non-drug group was 3.1 (95% CI = 2.3-4.3). Among women in the drug group, any smoking significantly increased the risk of poor fetal growth, prematurity, and admission to the special care nursery. In conclusion, innovative and effective strategies for tobacco cessation should target pregnant women as a high priority. Further research should identify the models of tobacco cessation most suited to women who also use other substances during pregnancy.