The annual health check for Aboriginal and Torres Strait Islander People has been welcomed as a means of conducting a comprehensive assessment to address preventive health care delivery, identify new diagnoses and initiate new treatments. Rates of health check uptake across Australia have been poor with less than 12% of the eligible population receiving one during 2009/10. This qualitative study sought to identify barriers and enablers to undertaking health checks in an urban Aboriginal Medical Service through semistructured interviews with 25 clinical staff (doctors, nurses and Aboriginal and Torres Strait Islander health workers). Clinical systems for conducting health checks were unclear to staff, with barriers relating to time pressures for both patients and clinic staff, and lack of clarity about staff responsibilities for initiating and conducting the health check. Additionally some staff perceived some content as sensitive, invasive, culturally inappropriate and of questionable value. Other barriers included concerns about community health literacy, disengagement with preventative health care, and suspicion about confidentiality and privacy. The development of clear service-wide systems that support the conduct of health checks are required to increase uptake, combined with supportive local clinical leadership and audit and feedback systems. Staff training, consideration of culture and roles, and critical review of health check content may improve staff confidence and community acceptance. Community-based health education and promotion is strongly supported by staff to increase client engagement, knowledge and acceptance of the health check.