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Background: By providing information on the relative merits and potential harms of the options available and a framework to clarify preferences, decision aids can improve knowledge and realistic expectations and decrease decisional conflict in individuals facing decisions between alternative forms of action. Decision-making about prenatal testing for fetal abnormalities is often confusing and difficult for women and the effectiveness of decision aids in this field has not been established. This study aims to test whether a decision aid for prenatal testing of fetal abnormalities, when compared to a pamphlet, improves women's informed decision-making and decreases decisional conflict. Methods/design: A cluster designed randomised controlled trial is being conducted in Victoria, Australia. Fifty General Practitioners (GPs) have been randomised to one of two arms: providing women with either a decision aid or a pamphlet. The two primary outcomes will be measured by comparing the difference in percentages of women identified as making an informed choice and the difference in mean decisional conflict scores between the two groups. Data will be collected from women using questionnaires at 14 weeks and 24 weeks gestation. The sample size of 159 women in both arms of the trial has been calculated to detect a difference of 18% (50 to 68%) in informed choice between the two groups. The required numbers have been adjusted to accommodate the cluster design, miscarriage and participant lost – to – follow up. Baseline characteristics of women will be summarised for both arms of the trial. Similarly, characteristics of GPs will be compared between arms. Differences in the primary outcomes will be analysed using 'intention-to-treat' principles. Appropriate regression techniques will adjust for the effects of clustering and include covariates to adjust for the stratifying variable and major potential confounding factors. Discussion: The findings from this trial will make a significant contribution to improving women's experience of prenatal testing and will have application to a variety of maternity care settings. The evaluation of a tailored decision aid will also have implications for pregnancy care providers by identifying whether or not such a resource will support their role in providing prenatal testing information.