This paper presents the view that policy-makers face scientific uncertainties in assessing the case for mandatory folate fortification as a policy response to epidemiological evidence of the relationship between folate and neural tube defects. Moreover, the resolution of these uncertainties is confounded by the under-resourced state of nutrition information systems in Australia and New Zealand. The uncertainties relate to potential risks and benefits associated with the intervention for the target group and the population in general. These risks and benefits reflect the mismatch between evidence and policy that arises when addressing a presumed genetic abnormality in at-risk individuals with an intervention that is population-wide in its scope. There is an urgent need to conduct ongoing national nutrition surveys and monitor and evaluate policy interventions to strengthen the capacity of nutrition information systems to inform decision-making for this current, and future, public health nutrition policy.