Community-based participatory research (CBPR) is often cited as a suitable methodological approach for academic researchers wanting to work collaboratively with Indigenous communities. This paper describes the Indigenous Resiliency Project currently being conducted in Redfern, Townsville and Perth. This case study is used to demonstrate how a group of university-based researchers and Aboriginal Community Controlled Health Services have used CBPR to work with young Indigenous Australians to explore young people’s perspectives on resilience in relation to bloodborne viruses and sexually transmissible infections. This paper also describes some initial benefits gained through the process of developing the Indigenous Resiliency CBPR Project, such as: developing research capacity; establishing relationships between community organisations and research institutions; and prioritising ethical and social considerations in the conduct of research. A community commentary on the experience of one health worker involved in the project accompanies the paper.