Background Sexually transmissible infection (STI) and blood-borne virus (BBV) notification data is a mainstay of the Australian National Notifiable Diseases Surveillance System (NNDSS) and is a mandatory requirement in all Australian jurisdictions. The system focuses on STI and BBV diagnoses alone, without testing, treatment or management data, leaving major gaps in the understanding of epidemics, especially among priority populations like Aboriginal and Torres Strait Islander peoples. Further information is required to supplement the NNDSS to better understand epidemics, the impact of interventions and health care delivery against clinical guidelines. Here we describe the rationale, processes and expected outcomes of establishing a national STI and BBV sentinel surveillance network in Aboriginal primary care services—known as the ATLAS network.Methods Researchers invited participation and consultation with Aboriginal Community-Controlled Health Services (ACCHS) clustered in five clinical hubs across four jurisdictions, representative of urban, regional and remote regions. Site-specific participation agreements were developed for each clinical hub and individual ACCHS. De-identified electronic medical record (EMR) data relating to STI and BBV testing, treatment and care are collected passively from each health service via the GRHANITE tm data extraction tool. These data are analysed centrally to inform 12 performance indicators which are included in surveillance reports generated for each health service and clinical hub.Results The ATLAS network currently involves 29 ACCHS representing all five clinical hubs. The ATLAS network provides detailed surveillance reports to individual ACCHS as well as contributing to aggregate comparative analyses at the clinical hub, jurisdictional and national levels. Data derived from the ATLAS network is used to assess clinical practice within each site. Aggregated data will inform clinical guidelines and extend the research potential of participating ACCHS sites. The ATLAS infrastructure can be expanded to include other health services and potentially linked to other data sources using GRHANITE.Conclusions The ATLAS network will supplement the NNDSS and contribute to improved understanding of local, regional and national patterns of clinical care of STI and BBV to inform clinical practice, policy, and program-planning.