Introduction Fetal alcohol spectrum disorder (FASD) is a significant public health concern. To prevent FASD, factors that place women at risk for giving birth to children with FASD must be investigated; however, there are little data in this area. This paper describes the development of the Manitoba mothers and FASD study, a retrospective cohort of mothers whose children were diagnosed with FASD, generated to investigate: (1) risk factors associated with giving birth to children with FASD; (2) maternal physical and health outcomes, as well as the usage of health and social services.

Methods The study population will be identified by linking children diagnosed with FASD from a provincially centralised FASD assessment clinic (from 31 March 1999 to 31 March 2012) to their birth mothers using de-identified administrative health data housed at the Manitoba Centre for Health Policy. Preliminary analysis has identified over 700 mothers, which is the largest sample size in this field to date. A comparison cohort of women with children who did not have an FASD diagnosis matched on the region of residence, date of birth of child with FASD and socioeconomic status will be generated to compare exposures and outcomes. Potential demographic, socioeconomic, family history, and physical and mental health risk factors will be investigated by linking a range of health and social databases, furthering insight into the root causes of drinking during pregnancy. The longitudinal data will allow us to document the usage patterns of healthcare and social services throughout significant periods in these women's lives to identify opportunities for prevention.

Ethics and dissemination Ethical approval has been obtained by the University of Manitoba's Health Research Ethics Board and the Manitoba Health Information Privacy Committee. Dissemination of study results will include engagement of stakeholders and policymakers through presentations and reports for policymakers, in parallel with scientific papers.