Objective: To establish baseline prevalence of neural tube defects (NTDs) prior to mandatory folic acid fortification in Australia. Method: Retrospective population based study. Data from the Australian Congenital Anomalies Monitoring System, for 1998–2005 were used to calculate birth prevalence including live/stillbirths of at least 20 weeks gestation or 400 g birthweight. Total prevalence and trends of NTD including terminations of pregnancy (TOPs) before 20 weeks were established using data from South Australia, Victoria and Western Australia because of the incomplete ascertainment in other states. Results: The birth prevalence of NTDs from 1998–2005, was 5/10,000 births. The total prevalence including TOPs was 13/10,000 births. A 26% declining trend in total prevalence was seen from 1992–2005, but the main decline occurred prior to 1998. Women who were Indigenous, socially disadvantaged, young, living in remote areas and had multiple gestations were more likely to give birth to babies with NTDs. Conclusion: The prevalence of NTD has been stable since 1998. Reporting of the birth prevalence alone underestimates the actual prevalence of NTD. Implications: From a public health perspective, future monitoring of NTD following implementation of fortification of bread‐making flour with folic acid should include a mixed methods approach; reporting birth prevalence on national data and total prevalence on tri‐state data.

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