Background Much attention in recent years has been given to the topic of public engagement in health technology assessment (HTA) decision-making. HTA organizations spend substantial resources and time on undertaking public engagement, and numerous studies have examined challenges and barriers to engagement in the decision-making process however uncertainty remains as to optimal methods to incorporate the views of the public in HTA decision-making. Little research has been done to ascertain whether current engagement processes align with public preferences and to what extent their desire for engagement is dependent on the question being asked by decision-makers or the characteristics of the decision. This study will examine public preferences for engagement in Australian HTA decision-making using an exploratory mixed methods design. Methods/Design The aims of this study are to: 1) identify characteristics about HTA decisions that are important to the public in determining whether public engagement should be undertaken on a particular topic, 2) determine which decision characteristics influence public preferences for the extent, or type of public engagement, and 3) describe reasons underpinning these preferences. Focus group participants from the general community, aged 18-70 years, will be purposively sampled from the Australian population to ensure a wide range of demographic groups. Each focus group will include a general discussion on public engagement as well as a ranking exercise using a modified nominal group technique (NGT). The NGT will inform the design of a discrete choice study to quantitatively assess public preferences for engagement in HTA decision-making. Discussion The proposed research seeks to investigate under what circumstances and how the public would like their views and preferences to be considered in health technology assessments. HTA organizations regularly make decisions about when and how public engagement should occur but without consideration of the public's preferences on the method and extent of engagement. This information has the potential to assist decision-makers in tailoring engagement approaches, and may be particularly useful in decisions with potential for conflict where clarification of public values and preferences could strengthen the decision-making process.