Neural tube defects (NTD) were 43% more common in Indigenous than in non-Indigenous infants in Western Australia in the 1980s, and there has been a fall in NTD overall in Western Australia since promotion of folate and voluntary fortification of food has occurred. In order to investigate whether the fall had occurred in both indigenous and non-Indigenous infants, data on NTD (births and terminations) were obtained from the WA Birth Defects Registry, and on all births from the Maternal and Child Health Research Data Base. Knowledge of folate was asked in a survey of indigenous women interviewed postpartum. Before the promotion of folate (1980–92), there has been a 42% increase in NTD in Indigenous compared with non-Indigenous infants (prevalence ratio (PR) = 1.42 [95% confidence interval (CI) 1.04, 1.94]); while in the most recent period (1996–2000), the prevalence in Indigenous infants was almost twice that of non-Indigenous infants (PR 1.98 [CI 1.25, 3.15]). Fifty-five per cent of Indigenous women knew about folate in pregnancy. Similar to sudden infant death syndrome, this study has highlighted health promotion that has been successful in reducing the risk of a childhood condition overall, but has failed to be effective for Indigenous children.