OBJECTIVES To estimate the prevalence of maternal substance use problems during the first 1000 days of children's lives, to inform planning and resourcing of antenatal screening and substance use in pregnancy services, alongside antenatal and postnatal health, parenting and social support services for pregnant women/new mothers and their babies.

METHOD This whole-population cohort was assembled from birth registration, perinatal and hospital data for children born 2008-2017, and their mothers, using data linked for the New South Wales (NSW) Child E-Cohort Project. The primary outcome was maternal substance use conditions and treatment recorded in six health, death and child protection data sources from the child's conception to age 2 years (the first 1000 days), including illicit substances, alcohol, opioid-agonist treatment and misuse of psychoactive medicines or substances.

RESULTS Of 970 470 children born to 625 856 mothers, 3.4% (N=32 647) had ≥1 maternal substance use problem records in the first 1000 days, including alcohol use (N=13 637; 1.4%) and other drug use (N=23 485; 2.4%). Maternal substance use problems were recorded during the pregnancy period for 1.4% of children, and from 28 to 1000 days postbirth for 2.7% of children. Outcome ascertainment was highest from child protection records (N=26 045), followed by mother's (N=10 793) then children's hospital records (N=3827). Child protection records more than doubled the prevalence of health and death records alone (1.4%). Social and health disadvantage was more common among children with maternal substance use problems.

CONCLUSIONS During the first 1000 days of life, 3.4% of NSW children had ≥1 maternal substance use problem recorded in health, child protection and death data sources. Child protection data enhance public health intelligence on the burden of maternal substance use problems among whole child populations. Near universal health system contact during pregnancy and birth is an opportunity to initiate early support for maternal substance use and co-occurring health and social disadvantage, to promote child health and development.